RNA-seq QC and motor neuron identities

Table S2 QC stats

Table S1 is iPSN differentiation protocols

multiqc_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), 
                                                                                                  # multiqc_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_stat_paths)
                                                                                                  ) %>% pull(multiqc_stat_paths)
multiqc_stats.tsv = multiqc_stat_paths %>% map(read_tsv, show_col_types = FALSE)                                                                        
names(multiqc_stats.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(dataset)
multiqc_data <- map_dfr(multiqc_stats.tsv, bind_rows, .id = "dataset") %>% clean_names() %>% drop_na(samtools_mqc_generalstats_samtools_flagstat_total) %>% filter(sample %in% ipsc_mn_als_datasets_with_lee.metadata$sample) %>%
  mutate(dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincs0" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS", dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~ dataset)) %>%
  select(dataset, sample, raw_total_sequences = samtools_mqc_generalstats_samtools_raw_total_sequences, flagstat_total = samtools_mqc_generalstats_samtools_flagstat_total, mapped_passed = samtools_mqc_generalstats_samtools_mapped_passed, reads_mapped = samtools_mqc_generalstats_samtools_reads_mapped, reads_mapped_percent = samtools_mqc_generalstats_samtools_reads_mapped_percent, reads_aligned = quali_map_mqc_generalstats_qualimap_reads_aligned, r_rna_percent = biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna, bias_5_3 = quali_map_mqc_generalstats_qualimap_5_3_bias, proper_pairs_percent = r_se_qc_mqc_generalstats_rseqc_proper_pairs_percent, reads_assigned_percent = feature_counts_mqc_generalstats_featurecounts_percent_assigned, reads_assigned = feature_counts_mqc_generalstats_featurecounts_assigned, percent_duplication = picard_mqc_generalstats_picard_percent_duplication, error_rate = samtools_mqc_generalstats_samtools_error_rate, non_primary_alignments = samtools_mqc_generalstats_samtools_non_primary_alignments, reads_properly_paired_percent = samtools_mqc_generalstats_samtools_reads_properly_paired_percent, percent_mapped = salmon_mqc_generalstats_salmon_percent_mapped, num_mapped = salmon_mqc_generalstats_salmon_num_mapped, uniquely_mapped_percent = star_mqc_generalstats_star_uniquely_mapped_percent, uniquely_mapped = star_mqc_generalstats_star_uniquely_mapped, percent_trimmed =cutadapt_mqc_generalstats_cutadapt_percent_trimmed, total_sequences = fast_qc_mqc_generalstats_fastqc_total_sequences, raw_percent_gc = fast_qc_raw_mqc_generalstats_fastqc_raw_percent_gc, raw_avg_sequence_length = fast_qc_raw_mqc_generalstats_fastqc_raw_avg_sequence_length, trimmed_percent_duplicates = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_duplicates, trimmed_percent_gc = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_gc)
kbl(multiqc_data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")

dataset	sample	raw_total_sequences	flagstat_total	mapped_passed	reads_mapped	reads_mapped_percent	reads_aligned	r_rna_percent	bias_5_3	proper_pairs_percent	reads_assigned_percent	reads_assigned	percent_duplication	error_rate	non_primary_alignments	reads_properly_paired_percent	percent_mapped	num_mapped	uniquely_mapped_percent	uniquely_mapped	percent_trimmed	total_sequences	raw_percent_gc	raw_avg_sequence_length	trimmed_percent_duplicates	trimmed_percent_gc
AnswerALS	CASE_NEUAA599TMX	90172968	110049375	110049375	90172968	100	45083935	0.0000341	0.99	67.98135	42.58702	23434669	0.143612	0.0024970	19876407	99.99435	100	24209931	92.84	42383420	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAB000NKC	89923754	126498124	126498124	89923754	100	44958805	0.0005546	0.98	53.83124	44.75184	28306923	0.209232	0.0027416	36574370	99.99317	100	29638747	89.01	40901591	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAE228FF6	130825845	271586963	271586963	130825845	100	65399474	0.0007375	0.98	22.06248	22.76193	30915467	0.514356	0.0017731	140761118	99.97944	100	33394237	79.24	53277634	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAE993EPR	125072312	165724188	165724188	125072312	100	62531785	0.0003629	1.01	54.17946	44.55271	36920158	0.254615	0.0020875	40651876	99.99301	100	39957256	88.95	56894281	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAF553MJ3	111693376	150525878	150525878	111693376	100	55843369	0.0007157	0.96	59.10802	33.41668	25151814	0.173674	0.0027145	38832502	99.99406	100	26254962	89.88	51139673	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAG241NUD	128635564	176979996	176979996	128635564	100	64313593	0.0002679	1.00	48.16291	37.53702	33218721	0.312094	0.0020796	48344432	99.99349	100	35528664	88.92	58281646	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAG603XLK	49130010	65504049	65504049	49130010	100	24563226	0.0000682	0.97	60.69713	40.28262	13194300	0.158176	0.0027302	16374039	99.99276	100	13971295	90.56	22629235	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAG766ULB	126929964	183940593	183940593	126929964	100	63460674	0.0001364	0.97	44.39181	36.66220	33721322	0.327647	0.0019348	57010629	99.99321	100	38009904	86.00	55851641	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAL076FCE	131833174	167516336	167516336	131833174	100	65912690	0.0001157	1.00	51.01627	46.44480	38903923	0.328565	0.0020416	35683162	99.99409	100	41680265	90.36	60722395	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAM655HF7	87433717	136427989	136427989	87433717	100	43714307	0.0007112	0.97	49.04198	35.24584	24043842	0.198245	0.0026647	48994272	99.99416	100	25533781	87.06	38824703	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAP285GGU	105486258	156711695	156711695	105486258	100	52739534	0.0001533	0.99	43.73658	32.45820	25434619	0.320706	0.0021994	51225437	99.99318	100	27807432	86.72	46727085	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAT234RK6	120938977	151644990	151644990	120938977	100	60463545	0.0000474	1.01	55.15200	41.70809	31627358	0.283175	0.0020793	30706013	99.99017	100	34225046	89.90	55453618	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAW157NMJ	114977089	145878754	145878754	114977089	100	57485309	0.0000300	0.98	62.68947	45.63163	33285218	0.176876	0.0026261	30901665	99.99437	100	34142140	92.00	53691857	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAW717TN6	126834297	159575177	159575177	126834297	100	63405958	0.0000835	1.00	58.45321	34.49994	27532068	0.239585	0.0019821	32740880	99.98235	100	28895482	90.26	58851386	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAX665ZHY	139537273	231443631	231443631	139537273	100	69763285	0.0002681	0.98	39.84617	29.65286	34317241	0.309280	0.0019313	91906358	99.99233	100	38214892	84.78	60401717	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAY067UTB	153856323	214267305	214267305	153856323	100	76923947	0.0005954	1.02	46.70964	36.05257	38626623	0.324427	0.0020446	60410982	99.99452	100	41699625	88.96	69716387	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUAZ394JEZ	134436051	178480252	178480252	134436051	100	67210701	0.0001388	1.00	48.50850	37.12241	33133119	0.328293	0.0022132	44044201	99.98910	100	37250812	86.85	60348215	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBA169GXD	123489072	183039179	183039179	123489072	100	61738330	0.0002351	1.01	47.16187	38.10750	34879845	0.270775	0.0019934	59550107	99.98995	100	37301727	85.89	54952243	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBC901KL3	128790984	158512044	158512044	128790984	100	64386445	0.0001962	0.99	58.53930	45.65992	36193674	0.253956	0.0019522	29721060	99.98595	100	37879352	91.83	60115760	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBC998WWB	135317031	201372187	201372187	135317031	100	67654064	0.0005399	0.97	46.27861	33.47649	33708237	0.280293	0.0020378	66055156	99.99342	100	35826821	87.60	60600596	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBD218YR3	94340954	144759706	144759706	94340954	100	47167578	0.0000192	0.98	48.05228	43.19240	31264298	0.227102	0.0027411	50418752	99.99385	100	34033859	87.16	41925594	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBD288RXQ	116501755	146458489	146458489	116501755	100	58246918	0.0002148	0.94	60.91542	28.60820	20951015	0.209542	0.0021196	29956734	99.99320	100	21670764	91.97	54377155	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBK117YXL	124612330	176723226	176723226	124612330	100	62302088	0.0011893	1.00	50.17024	34.82647	30775311	0.258965	0.0021462	52110896	99.99346	100	32249185	88.26	56369904	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBM949LA5	123889216	181640803	181640803	123889216	100	61938822	0.0003055	1.00	45.47430	36.03590	32731139	0.303790	0.0020690	57751587	99.99066	100	35619732	87.21	55164621	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBN979ZZ5	121537754	158678819	158678819	121537754	100	60763327	0.0000682	1.01	54.39141	44.35331	35193014	0.260889	0.0018488	37141065	99.99087	100	38577212	89.17	55260530	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBT273FH3	110747555	139595936	139595936	110747555	100	55368342	0.0002129	1.01	51.51089	49.11158	34282757	0.326915	0.0019341	28848381	99.99018	100	38296907	89.49	50443790	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBW008RJ5	148445384	191169979	191169979	148445384	100	74215056	0.0000695	1.00	53.75423	42.16076	40303598	0.281581	0.0020311	42724595	99.98971	100	43213983	90.70	68428153	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUBY734PFR	89534532	117260923	117260923	89534532	100	44764400	0.0002683	0.96	61.13324	42.59420	24974733	0.168385	0.0027772	27726391	99.99360	100	26194066	90.53	41347426	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCB613CA9	120314012	157070980	157070980	120314012	100	60153084	0.0001226	0.98	55.67521	38.41598	30172303	0.247442	0.0019572	36756968	99.99348	100	32529148	89.89	55041136	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCD502BFU	122416921	163718351	163718351	122416921	100	61200013	0.0002703	0.98	52.61787	44.28361	36255523	0.268173	0.0020632	41301430	99.98620	100	37130970	90.10	56342440	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCE965ZGK	99739464	146713178	146713178	99739464	100	49866419	0.0000423	0.97	51.30799	41.90401	30741292	0.211673	0.0026514	46973714	99.99336	100	32466869	88.12	44747465	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCF538BRM	124776812	147487594	147487594	124776812	100	62382563	0.0000829	0.98	64.21820	40.91160	30172840	0.218006	0.0021087	22710782	99.99063	100	31309221	92.23	58712724	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCG511MJ6	141403477	188997248	188997248	141403477	100	70694493	0.0001681	0.97	50.33612	39.01470	36872585	0.301172	0.0022295	47593771	99.98975	100	39203261	88.35	64401376	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCN596RR3	107638838	136547448	136547448	107638838	100	53815848	0.0002137	0.97	63.39855	39.05644	26667044	0.168394	0.0027305	28908610	99.99336	100	28293153	91.27	49945306	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCP218XVV	133693665	206523773	206523773	133693665	100	66837184	0.0005851	0.97	43.34389	36.40578	37599113	0.298408	0.0020207	72830108	99.98557	100	39426915	85.76	59265499	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCT022VTK	139555913	173337477	173337477	139555913	100	69771316	0.0000122	0.96	56.24646	47.25522	40959489	0.277179	0.0020943	33781564	99.99048	100	42662232	91.68	64970108	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCT842RJV	132288250	170017088	170017088	132288250	100	66141468	0.0000451	0.98	48.80887	49.59928	42165473	0.348855	0.0018535	37728838	99.99598	100	47530437	89.52	60131099	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCU076ADN	138846225	192907404	192907404	138846225	100	69417377	0.0004188	0.99	47.60645	44.06356	42504669	0.310876	0.0018324	54061179	99.99174	100	45038105	88.31	62770985	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCU245GBQ	89412399	120947846	120947846	89412399	100	44703436	0.0000910	0.96	57.40010	45.43816	27479901	0.193442	0.0027497	31535447	99.99382	100	29510050	89.99	40911080	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUCV578DFJ	111373277	166478871	166478871	111373277	100	55679121	0.0002071	0.98	41.35444	32.47711	27037653	0.353243	0.0021349	55105594	99.98650	100	30515895	84.67	48770148	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDD018KAH	88045557	122378672	122378672	88045557	100	44020125	0.0003412	0.99	55.66305	44.06664	26965653	0.196328	0.0026667	34333115	99.99397	100	28593991	89.49	40078342	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDE902GCT	99937040	135441084	135441084	99937040	100	49965149	0.0002740	0.99	57.04999	46.88175	31750639	0.195966	0.0027189	35504044	99.99325	100	33903856	89.67	45708501	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDG000ZG5	100589599	165876997	165876997	100589599	100	50291866	0.0006254	0.99	46.05712	27.37350	22704273	0.205570	0.0027085	65287398	99.99417	100	24022760	86.49	44142529	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDG272XWC	119792730	177927759	177927759	119792730	100	59890533	0.0006492	1.00	44.32943	35.83447	31883115	0.312701	0.0019648	58135029	99.99026	100	36165777	85.26	52442197	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDH063DEA	105591880	147314413	147314413	105591880	100	52792270	0.0001292	0.97	43.49162	44.14237	32517163	0.368034	0.0018514	41722533	99.99305	100	34872581	88.71	47660863	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDM949BAR	128202048	287681995	287681995	128202048	100	64098089	0.0001448	1.03	25.96516	19.68364	28314124	0.380233	0.0022874	159479947	99.99542	100	32796971	77.47	51012285	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDP155HFH	139462948	169095371	169095371	139462948	100	69727255	0.0001219	0.98	60.02936	46.56030	39368193	0.248814	0.0018828	29632423	99.99395	100	42287242	91.81	64911812	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDT709YHN	98823893	124576566	124576566	98823893	100	49409281	0.0001435	1.01	62.71525	43.64291	27185855	0.182869	0.0025115	25752673	99.99461	100	29035636	91.79	45965043	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDY534KGP	141589390	224129099	224129099	141589390	100	70790345	0.0005739	0.98	38.78086	31.40492	35195960	0.357183	0.0021470	82539709	99.99386	100	38758487	85.07	61667082	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUDZ473EGM	154600775	199257878	199257878	154600775	100	77292269	0.0001501	0.98	54.35758	42.13185	41979848	0.273593	0.0020343	44657103	99.98950	100	45298101	89.96	70716346	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEB422WW0	130660148	179922487	179922487	130660148	100	65326217	0.0002187	0.97	55.14692	45.24011	40700856	0.211997	0.0026283	49262339	99.99410	100	42774565	89.96	59731414	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEC400NYR	125412392	189213757	189213757	125412392	100	62698769	0.0000618	0.98	46.63567	32.48969	30741078	0.263394	0.0020064	63801365	99.98816	100	33532156	85.61	55448738	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEK191WYC	106345287	143788123	143788123	106345287	100	53169399	0.0003434	0.99	56.49555	44.95985	32325352	0.206117	0.0025269	37442836	99.99390	100	34889663	89.84	48514495	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEM029XXZ	93028028	116184964	116184964	93028028	100	46511187	0.0000987	0.98	64.36809	45.35590	26350014	0.168057	0.0025941	23156936	99.99392	100	27645965	91.84	43343592	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEM720BUU	86141784	131324319	131324319	86141784	100	43068135	0.0002889	0.97	46.29251	40.06190	26307070	0.259890	0.0029109	45182535	99.99360	100	29496177	86.04	37987180	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEN017PCJ	130567564	222562143	222562143	130567564	100	65279499	0.0005546	0.98	38.82526	29.48605	32814502	0.304728	0.0020111	91994579	99.99344	100	35304279	84.03	56203623	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEN476CLW	93313194	124980814	124980814	93313194	100	46653389	0.0002496	0.98	58.79835	45.51679	28445515	0.179232	0.0028058	31667620	99.99312	100	30075286	90.15	42774630	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUET072VDG	141595402	188283258	188283258	141595402	100	70794354	0.0001037	1.00	48.77956	45.04774	42410775	0.326791	0.0020269	46687856	99.99527	100	46245461	89.47	64389846	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEU318NY2	134884750	201782160	201782160	134884750	100	67439023	0.0003835	1.01	43.29325	34.36975	34677910	0.323295	0.0020267	66897410	99.99503	100	38364153	86.00	59255159	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEU558MNK	100521886	138251806	138251806	100521886	100	50257610	0.0002044	1.00	58.04566	40.34897	27893309	0.172240	0.0027409	37729920	99.99337	100	28934684	90.09	46268251	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUEY478NZP	123856364	161856132	161856132	123856364	100	61925206	0.0001457	1.01	49.49657	48.32963	39114279	0.326938	0.0018693	37999768	99.99519	100	43542860	89.22	56068266	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFB989DT1	97111909	119493426	119493426	97111909	100	48553082	0.0003310	0.98	65.46732	42.98284	25682366	0.167866	0.0025665	22381517	99.99408	100	27242345	92.20	45373156	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFH122WN7	139072399	163898369	163898369	139072399	100	69531586	0.0000398	0.98	64.35023	36.80086	30160047	0.219188	0.0019883	24825970	99.99337	100	30026682	93.49	65888103	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFH461AAN	136572099	178778483	178778483	136572099	100	68282467	0.0002066	0.99	51.64257	38.98675	34851914	0.298697	0.0023940	42206384	99.99475	100	37275738	89.44	62183816	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFU395MJD	106078669	150927010	150927010	106078669	100	53033252	0.0003335	0.97	46.37928	36.14942	27282828	0.311878	0.0020394	44848341	99.98853	100	30319443	87.29	47215106	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFV237VCZ	116591551	142251705	142251705	116591551	100	58289922	0.0000931	0.98	60.75871	40.78029	29008424	0.233622	0.0020568	25660154	99.98996	100	29905603	91.78	54588104	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFX386KMB	136454440	179241166	179241166	136454440	100	68222312	0.0000788	0.98	52.12221	43.88143	39329613	0.289722	0.0020814	42786726	99.99281	100	42433048	89.66	62381253	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUFY342UNG	118184565	150571375	150571375	118184565	100	59087606	0.0001005	0.99	58.35599	38.33532	28863430	0.230310	0.0018508	32386810	99.99209	100	31272225	89.91	54126474	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGD965XVD	136583771	169896591	169896591	136583771	100	68287240	0.0002035	1.02	59.11176	45.68885	38814619	0.241102	0.0019518	33312820	99.99320	100	40989816	91.63	63555884	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGE540TC4	75422741	95453478	95453478	75422741	100	37708985	0.0004707	1.00	64.92686	41.39750	19758910	0.150972	0.0026750	20030737	99.99367	100	20586436	91.90	35209660	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGH995TFK	133045485	181931315	181931315	133045485	100	66515692	0.0000703	0.97	45.06227	42.23993	38428248	0.358487	0.0017872	48885830	99.98940	100	42594183	87.29	59472955	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGJ081HKR	92827431	129592427	129592427	92827431	100	46411223	0.0002330	0.99	55.89339	40.40376	26181432	0.187137	0.0026103	36764996	99.99463	100	28115190	89.63	42254938	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGL543NJ1	122243099	155846140	155846140	122243099	100	61116951	0.0001317	1.01	57.60356	38.98401	30380271	0.239767	0.0019417	33603041	99.99248	100	32357464	90.50	56279458	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGP781PDU	99089507	123260123	123260123	99089507	100	49542192	0.0000507	0.97	63.37958	48.03670	29606571	0.184248	0.0024666	24170616	99.99483	100	31353374	91.95	46168118	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGR121TFD	141091397	199599129	199599129	141091397	100	70536352	0.0001659	0.98	49.49694	36.83002	36761388	0.270829	0.0021551	58507732	99.98675	100	38723194	86.77	63614335	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGR539MVT	134594246	172095822	172095822	134594246	100	67286121	0.0001557	1.00	52.87871	45.50994	39167316	0.300302	0.0021235	37501576	99.98365	100	42249514	89.43	61521240	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGW326BRV	86942871	119710782	119710782	86942871	100	43469101	0.0002033	0.98	56.16165	39.44430	23610810	0.195022	0.0026380	32767911	99.99463	100	25361092	89.90	39656424	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUGW340YEB	136692973	183476162	183476162	136692973	100	68340429	0.0000880	1.00	51.60555	38.39680	35227745	0.279955	0.0019997	46783189	99.99114	100	38284910	89.09	62053078	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHB491NGF	145522197	202221470	202221470	145522197	100	72753784	0.0002094	0.96	50.41580	31.63419	31988783	0.272387	0.0020442	56699273	99.98995	100	32812161	89.01	66227888	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHG644RYB	138979998	201813224	201813224	138979998	100	69482706	0.0001692	1.01	45.87918	38.66221	39017272	0.304173	0.0018454	62833226	99.98950	100	43918370	85.05	60646533	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHG791RV5	119400996	160767092	160767092	119400996	100	59697027	0.0000261	0.99	56.18658	42.85333	34448962	0.214817	0.0025435	41366096	99.99419	100	36903652	90.01	54523059	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHK991AVP	150076387	203632648	203632648	150076387	100	75035119	0.0003553	0.99	45.16991	45.32742	46152868	0.363986	0.0018715	53556261	99.99590	100	51372601	88.06	67327991	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHL999WWT	120914707	152068342	152068342	120914707	100	60453335	0.0002409	0.99	58.29780	42.58072	32378390	0.242050	0.0020147	31153635	99.99335	100	34087609	91.26	56126841	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHM532NDD	132018194	177570876	177570876	132018194	100	66004538	0.0005658	0.99	53.15327	33.04001	29336787	0.257687	0.0020835	45552682	99.99309	100	31431334	89.17	60004909	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHT569HT1	135726690	175838065	175838065	135726690	100	67856787	0.0001545	0.98	53.70584	36.81147	32367583	0.278507	0.0021176	40111375	99.99034	100	34696832	89.43	62178209	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHV216EHA	137327199	187736616	187736616	137327199	100	68658564	0.0011124	0.96	51.74819	31.40976	29486017	0.266897	0.0020767	50409417	99.99267	100	31516294	88.75	62223182	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHW530WD8	142706149	186097772	186097772	142706149	100	71346968	0.0001573	0.98	54.96032	43.72086	40685469	0.257348	0.0020625	43391623	99.99144	100	42259547	90.23	65688979	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHW590KBH	87895366	120494665	120494665	87895366	100	43945090	0.0001100	0.98	57.59010	39.21984	23630275	0.178782	0.0025832	32599299	99.99410	100	25159813	89.88	40130196	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHY206ZEQ	112630093	177166290	177166290	112630093	100	56312448	0.0012134	0.99	39.86670	38.70032	34283660	0.342164	0.0019487	64536197	99.99539	100	38206988	85.64	49149528	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUHZ302VU4	84819581	110724093	110724093	84819581	100	42407446	0.0003190	1.00	58.77952	51.52982	28529537	0.203833	0.0025028	25904512	99.99447	100	30685204	90.34	38920358	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJA217MTJ	138544788	180023548	180023548	138544788	100	69268627	0.0001135	1.01	61.97741	29.35444	26423870	0.168603	0.0026456	41478760	99.99456	100	27865782	91.26	64185561	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJA666PYD	104992916	179578594	179578594	104992916	100	52492856	0.0001505	0.97	42.87717	30.33617	27240233	0.229110	0.0027915	74585678	99.99314	100	29473424	84.84	45410352	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJC191RLE	134351533	169112893	169112893	134351533	100	67171099	0.0004095	0.99	58.06424	36.96069	31254937	0.244700	0.0020588	34761360	99.99305	100	33284137	90.83	62105731	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJG311WGV	129764735	173924387	173924387	129764735	100	64879037	0.0002634	0.98	50.35555	38.41671	33409743	0.299301	0.0020763	44159652	99.99487	100	37635711	88.24	58253244	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJG885PY7	141363192	207769282	207769282	141363192	100	70672574	0.0004961	0.99	45.29718	35.89114	37290108	0.305882	0.0021327	66406090	99.98724	100	39751751	86.43	62682976	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJH197AK2	109692064	148477602	148477602	109692064	100	54840601	0.0000835	1.01	50.42878	48.36931	35912880	0.290581	0.0018832	38785538	99.99010	100	39219267	88.36	49489164	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJK720JCL	145196285	176658442	176658442	145196285	100	72593038	0.0001203	0.98	58.35053	41.40399	36574311	0.266350	0.0022999	31462157	99.99297	100	38573347	92.26	67904327	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJL547WVQ	122518635	147759823	147759823	122518635	100	61252132	0.0000491	1.07	56.70514	46.87074	34632151	0.292459	0.0018165	25241188	99.98827	100	35492615	92.56	57611614	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJL595JAZ	125569663	167641984	167641984	125569663	100	62781255	0.0001647	1.00	49.09008	39.12172	32794270	0.317243	0.0024428	42072321	99.99430	100	35920670	88.09	56604191	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJP935AVF	133932079	201524424	201524424	133932079	100	66962632	0.0004649	0.99	42.24562	30.52310	30757338	0.337322	0.0021899	67592345	99.99491	100	34475263	85.68	58630869	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJX780XXK	132644761	163932667	163932667	132644761	100	66316933	0.0001693	1.00	59.09920	38.90757	31893879	0.245205	0.0019813	31287906	99.99179	100	32976255	91.64	61928100	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJX990GR5	152756972	180280188	180280188	152756972	100	76370797	0.0003500	0.98	60.56161	38.67019	34861001	0.262740	0.0019740	27523216	99.98993	100	37160120	92.49	71699955	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJY426MBU	163506082	212057895	212057895	163506082	100	81747885	0.0000659	0.96	55.88217	38.63594	40967948	0.250772	0.0019916	48551813	99.99369	100	42713301	90.91	75805318	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUJY536DKF	130996985	161559410	161559410	130996985	100	65493732	0.0001393	0.96	59.05377	42.66486	34467201	0.247774	0.0020449	30562425	99.99273	100	36355288	91.51	60915279	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKA860NUG	95743148	149986716	149986716	95743148	100	47868100	0.0004797	0.99	39.72778	32.51799	24388292	0.343615	0.0022024	54243568	99.99274	100	28045765	83.39	41004845	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKD025JPF	73470692	95420234	95420234	73470692	100	36733163	0.0003883	1.00	61.46689	46.42426	22150320	0.170845	0.0026557	21949542	99.99406	100	23648413	91.00	33925482	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKP160HX8	158114922	219097462	219097462	158114922	100	79053571	0.0000658	1.00	44.77145	40.20348	44044684	0.354843	0.0020222	60982540	99.99508	100	48852294	87.81	70714096	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKR376CW3	137592744	180066208	180066208	137592744	100	68793025	0.0002550	1.01	52.27950	38.76256	34901012	0.291103	0.0020278	42473464	99.99513	100	37955194	89.17	62403770	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKV547CFA	106270699	173079851	173079851	106270699	100	53131757	0.0001257	1.01	37.97373	32.16386	27836633	0.347247	0.0020279	66809152	99.99324	100	32569899	82.44	45019350	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUKY704JVA	111957315	145492330	145492330	111957315	100	55973716	0.0006706	0.99	53.27409	44.06555	32059068	0.281775	0.0018965	33535015	99.99117	100	34918698	88.69	51063996	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULA694DDC	144121470	210976422	210976422	144121470	100	72052030	0.0001136	0.99	32.83201	39.23243	41391076	0.496468	0.0019312	66854952	99.98792	100	46414165	85.78	63306620	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULA777DBT	145235062	185554062	185554062	145235062	100	72609573	0.0001060	0.99	57.47245	38.64274	35855491	0.238996	0.0021044	40319000	99.98904	100	37728047	90.04	66935925	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULD354RZB	130303603	171222929	171222929	130303603	100	65147360	0.0000794	0.99	52.14630	39.73101	34017084	0.290105	0.0019778	40919326	99.99318	100	37816668	88.81	58989271	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULH729AU2	132185143	188457240	188457240	132185143	100	66082206	0.0000322	1.02	33.72764	32.90749	31013438	0.497084	0.0022970	56272097	99.98432	100	33250669	86.85	59187708	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULL588ALG	101192464	129328744	129328744	101192464	100	50592428	0.0004602	1.03	62.52614	40.65428	26290767	0.171396	0.0025575	28136280	99.99248	100	27554179	91.05	46819320	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULL648LJ1	152013999	189349623	189349623	152013999	100	75998771	0.0003482	0.99	56.32040	46.09657	43647051	0.275342	0.0021868	37335624	99.98917	100	47298299	90.61	70333861	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULP998KDJ	101414493	129829996	129829996	101414493	100	50702318	0.0001817	1.00	57.38737	39.83596	25862178	0.238810	0.0019215	28415503	99.99028	100	27433069	90.22	46667209	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULT851ENP	141787116	182679467	182679467	141787116	100	70890034	0.0000863	0.98	52.31735	45.64324	41692465	0.301362	0.0019864	40892351	99.99503	100	44820562	90.51	65314488	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULY177TTN	88184032	140832260	140832260	88184032	100	44089217	0.0001702	0.98	45.99328	35.86896	25258960	0.229827	0.0026625	52648228	99.99365	100	27538571	85.82	38673250	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULY328CRJ	124827649	178583027	178583027	124827649	100	62409884	0.0001362	0.99	45.38943	39.45594	35233132	0.322612	0.0020742	53755378	99.99369	100	38907414	87.51	55659392	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEULZ548ZXV	116550540	157670085	157670085	116550540	100	58269845	0.0006271	1.02	50.82802	39.63846	31252626	0.285243	0.0021817	41119545	99.99069	100	34000171	88.43	52791572	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUMB242CLN	146219969	188982330	188982330	146219969	100	73094377	0.0001099	0.97	53.25336	41.38281	39111622	0.285622	0.0020325	42762361	99.97865	100	42594423	89.14	66786201	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUME498PCJ	121179342	166957105	166957105	121179342	100	60586895	0.0003321	0.98	53.63860	38.22758	31913320	0.232192	0.0024516	45777763	99.99542	100	35558756	88.60	54433039	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUMH634MKT	149214391	209805138	209805138	149214391	100	74603299	0.0020155	1.02	46.51324	39.06467	40982048	0.318690	0.0020759	60590747	99.99478	100	44454595	87.85	66723213	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUMN012EVP	122953745	152285269	152285269	122953745	100	61473583	0.0004007	0.97	60.87585	40.63853	30944925	0.222147	0.0019786	29331524	99.99465	100	32093482	92.10	57458694	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUMW598YMT	148697107	211131558	211131558	148697107	100	74341725	0.0004545	0.97	45.45767	35.42568	37401266	0.327205	0.0021479	62434451	99.99082	100	40987087	86.39	66263817	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUMY871DGF	139888957	164950585	164950585	139888957	100	69938355	0.0000798	0.99	64.38220	41.02218	33836284	0.218205	0.0019914	25061628	99.99125	100	35805638	92.48	65655990	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNA248WXL	87881681	112756521	112756521	87881681	100	43938255	0.0003365	0.98	63.36786	37.94840	21395900	0.158051	0.0026177	24874840	99.99412	100	22601559	91.86	40898290	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNG326MFP	141420621	188366517	188366517	141420621	100	70704595	0.0001198	0.97	51.47303	40.77300	38404802	0.288874	0.0019689	46945896	99.99192	100	41918606	89.03	64097084	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNJ155KYL	139821585	183237512	183237512	139821585	100	69907930	0.0001016	1.03	50.34089	44.02644	40338225	0.315424	0.0018692	43415927	99.99591	100	44436014	89.26	63359785	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNJ938DUL	110373409	146981217	146981217	110373409	100	55180998	0.0002221	1.01	49.53905	42.27752	31073805	0.313882	0.0020983	36607808	99.98966	100	34163950	87.65	49706589	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNL303HLF	125099316	228966770	228966770	125099316	100	62546398	0.0001992	1.00	32.27064	29.37712	33633585	0.378200	0.0020683	103867454	99.99479	100	36878172	82.03	52488696	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNL415AFW	92867967	133667390	133667390	92867967	100	46431277	0.0008440	0.97	52.02197	42.72272	28554762	0.219845	0.0027121	40799423	99.99417	100	30330975	88.33	41786405	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNR020KV6	115301323	164150667	164150667	115301323	100	57647868	0.0002172	0.97	46.35115	37.01777	30383974	0.312230	0.0020360	48849344	99.99515	100	33596521	87.46	51460383	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUNZ171UYF	155580787	201349190	201349190	155580787	100	77786615	0.0000477	1.00	54.53630	41.63565	41918494	0.268249	0.0020768	45768403	99.99514	100	43804088	90.97	71885848	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPG593UTV	126721699	179908913	179908913	126721699	100	63355853	0.0002942	0.98	43.44807	36.26768	32627194	0.356489	0.0021263	53187214	99.99211	100	36485890	86.39	56098842	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPK546ZLD	127719209	173514278	173514278	127719209	100	63853530	0.0006982	0.98	52.70728	41.76322	36236208	0.255609	0.0019434	45795069	99.99049	100	38892514	88.95	58161535	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPM937TMY	114752546	154017532	154017532	114752546	100	57373291	0.0001371	1.00	48.91011	40.73999	31375051	0.317677	0.0020453	39264986	99.99480	100	33677004	89.09	52119903	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPN525XEW	100061085	152901938	152901938	100061085	100	50027523	0.0011091	0.96	48.26096	37.85523	28942287	0.229381	0.0027257	52840853	99.99396	100	30587704	86.88	44430092	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPR357AUF	140600115	188629695	188629695	140600115	100	70294764	0.0003826	1.01	50.96441	42.12141	39730312	0.290189	0.0020325	48029580	99.99247	100	42959648	88.51	63541475	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPR600MBU	101661612	157059475	157059475	101661612	100	50828202	0.0006545	0.95	47.55700	38.91106	30558182	0.231348	0.0025577	55397863	99.99488	100	33189766	87.17	45072415	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUPY050ANK	125092895	173092975	173092975	125092895	100	62538321	0.0008399	0.97	47.48535	37.00170	32028248	0.316107	0.0021859	48000080	99.98701	100	34791092	87.00	56250544	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURA639MK8	88681385	174800313	174800313	88681385	100	44338192	0.0002404	0.99	35.38047	26.17944	22881914	0.261938	0.0026667	86118928	99.99436	100	25273046	81.23	36696280	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURF720KHA	127645475	214650164	214650164	127645475	100	63818250	0.0001552	1.02	37.19388	30.61430	32858913	0.341368	0.0020499	87004689	99.99297	100	36233250	84.23	54948319	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURJ362MXH	128821381	164937784	164937784	128821381	100	64406009	0.0002776	0.99	54.82691	32.31893	26655251	0.273043	0.0020595	36116403	99.99273	100	28257434	90.79	59538230	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURR881FKY	107640056	139900164	139900164	107640056	100	53817142	0.0001954	0.97	59.88210	38.77847	27126995	0.192805	0.0024546	32260108	99.99464	100	29184368	90.84	49514621	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURX315DYH	105760532	182500083	182500083	105760532	100	52875618	0.0002318	1.00	38.24761	32.14216	29332003	0.304415	0.0019613	76739551	99.99121	100	31862596	84.81	45743652	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEURX909UL6	101253707	143049397	143049397	101253707	100	50623663	0.0003391	0.99	52.97698	43.28501	30961318	0.218807	0.0026655	41795690	99.99370	100	33363015	88.75	45735585	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTA057AF6	145972936	182832898	182832898	145972936	100	72981892	0.0001730	0.98	57.41441	42.36811	38733887	0.255461	0.0019554	36859962	99.99373	100	39947509	92.03	68030270	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTA689LN5	97978631	137960489	137960489	97978631	100	48986369	0.0000766	0.99	54.36726	45.44476	31349678	0.201869	0.0026863	39981858	99.99399	100	33057528	89.27	44471077	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTB230DA3	127287620	167555194	167555194	127287620	100	63638375	0.0002299	0.99	51.77864	44.64902	37410054	0.293582	0.0021534	40267574	99.99146	100	41078024	88.53	57735990	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTC791PVE	145218429	194002781	194002781	145218429	100	72602394	0.0001546	0.96	48.45311	42.66868	41393810	0.326557	0.0020144	48784352	99.99061	100	45961276	87.67	65228107	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTD314VFT	118694774	199503383	199503383	118694774	100	59340190	0.0003396	1.01	40.55880	28.63025	28562306	0.283515	0.0019801	80808609	99.98787	100	31769329	84.10	51072663	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTD713DE3	111654521	157067140	157067140	111654521	100	55824002	0.0001290	0.98	52.91439	42.42968	33323420	0.224722	0.0027149	45412619	99.99416	100	35928817	89.06	50602796	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTD866EAH	124436305	180663402	180663402	124436305	100	62210277	0.0002514	0.98	44.24790	38.73755	34997730	0.329244	0.0021389	56227097	99.98734	100	39272084	85.83	54881137	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTJ613AH9	72472964	98310077	98310077	72472964	100	36233970	0.0002277	0.99	59.58567	35.73748	17567925	0.161272	0.0026973	25837113	99.99307	100	18303686	90.13	33289122	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTL257PNR	132701657	180494960	180494960	132701657	100	66347623	0.0002861	1.00	49.20961	39.11086	35298356	0.304793	0.0020186	47793303	99.99517	100	37791840	88.97	60066049	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTL699WJ0	114658516	144969594	144969594	114658516	100	57324735	0.0010707	0.97	56.07008	44.57791	32315111	0.266599	0.0019060	30311078	99.99211	100	35710392	89.86	52348367	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTM934BPY	129527421	171464767	171464767	129527421	100	64759198	0.0015967	1.00	53.80390	36.74346	31503263	0.261451	0.0020043	41937346	99.99303	100	34456215	89.53	59086995	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTN952DDG	105873411	166179344	166179344	105873411	100	52933748	0.0003591	0.99	46.94140	33.50951	27844308	0.231224	0.0025588	60305933	99.99441	100	29696227	86.83	46944485	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUTU360YJY	116118985	143509356	143509356	116118985	100	58052735	0.0001467	1.01	57.95106	53.19941	38177862	0.259297	0.0017220	27390371	99.98836	100	41726408	90.06	53322943	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUC458RFT	129847013	194034481	194034481	129847013	100	64917516	0.0001199	1.02	41.97888	34.38410	33362263	0.343356	0.0020920	64187468	99.99077	100	37273830	84.20	56817414	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUD158CJF	104670750	132835531	132835531	104670750	100	52328344	0.0000158	0.97	53.12357	47.52401	31569214	0.300438	0.0018088	28164781	99.98657	100	35081615	88.71	47698947	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUE852BB1	87313527	122251990	122251990	87313527	100	43654085	0.0000895	0.98	54.63034	43.88646	26827563	0.201953	0.0025186	34938463	99.99386	100	28952491	88.87	39423970	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUF613PHL	126490792	162878061	162878061	126490792	100	63241442	0.0000430	0.97	52.54516	42.82306	34877131	0.298866	0.0021813	36387269	99.99375	100	38470412	89.41	57733762	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUH658EYH	121126070	181119012	181119012	121126070	100	60560176	0.0006071	1.00	41.82229	39.10448	35414672	0.346869	0.0019553	59992942	99.99528	100	40091692	85.86	53030800	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUJ507EAB	114321103	144750000	144750000	114321103	100	57157204	0.0000440	1.06	53.63220	47.14457	34123017	0.296042	0.0015816	30428897	99.99414	100	37643813	89.78	52034154	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUL256UC9	119837015	165056579	165056579	119837015	100	59911454	0.0001191	0.98	53.36755	30.51364	25185391	0.235516	0.0021328	45219564	99.98823	100	27258314	87.95	54168228	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUL292XRC	104836431	156852741	156852741	104836431	100	52409181	0.0003069	1.00	43.89086	33.23504	26069986	0.311924	0.0019622	52016310	99.98276	100	29882387	84.80	45819278	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUL311NRQ	144461771	187508051	187508051	144461771	100	72226897	0.0001483	1.03	51.75003	41.70654	39103731	0.303675	0.0019373	43046280	99.99448	100	42363669	90.08	66008915	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUP280KXL	118516272	156079810	156079810	118516272	100	59254381	0.0001999	0.99	54.93796	41.02595	32018652	0.250312	0.0019529	37563538	99.99366	100	33948150	89.62	54110646	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUU506WZF	138573134	292249673	292249673	138573134	100	69279224	0.0006337	0.99	29.33627	18.68155	27300803	0.342525	0.0023071	153676539	99.98940	100	30195009	78.78	56290277	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUUZ216XY8	117115830	153394704	153394704	117115830	100	58553043	0.0003654	1.01	53.12807	42.10338	32295500	0.276408	0.0019538	36278874	99.99168	100	35552913	89.03	53409559	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVD687XD8	127850466	196983862	196983862	127850466	100	63918317	0.0002929	1.01	41.30500	33.27007	32772166	0.333570	0.0022399	69133396	99.98918	100	36669301	84.14	55483568	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVF888UHM	87839503	123440383	123440383	87839503	100	43916958	0.0008791	1.01	55.05094	38.51858	23775161	0.194150	0.0027037	35600880	99.99364	100	25076486	88.39	39713751	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVJ560JGZ	145026604	169004770	169004770	145026604	100	72508859	0.0001747	0.99	66.23438	37.93196	32055485	0.205332	0.0020462	23978166	99.99387	100	32639281	93.31	68598571	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVM674HUA	112397326	158281937	158281937	112397326	100	56194993	0.0001695	1.00	50.24582	44.73241	35403908	0.263150	0.0026860	45884611	99.99347	100	38967578	87.97	50368377	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVN746WKV	113418563	166319216	166319216	113418563	100	56705806	0.0000901	1.00	48.88816	38.69327	32179025	0.250970	0.0026661	52900653	99.99387	100	34899811	87.12	50451695	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVP060WFG	144863978	187399644	187399644	144863978	100	72426514	0.0000170	0.99	49.74931	43.87856	41117626	0.333074	0.0020505	42535666	99.99244	100	45474655	88.88	65686991	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVR636VTP	128629292	171359932	171359932	128629292	100	64309737	0.0001487	1.00	53.73263	38.45949	32954754	0.258677	0.0020067	42730640	99.99237	100	35787049	89.32	58705014	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVR814YCY	144773359	197542865	197542865	144773359	100	72382408	0.0004202	1.00	50.77449	33.73113	33318593	0.281012	0.0023057	52769506	99.99410	100	34471604	89.47	65992995	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVU735HU6	123502082	187698709	187698709	123502082	100	61747675	0.0003588	0.99	42.95702	34.74852	32612974	0.315037	0.0023181	64196627	99.99455	100	34653270	86.96	54922335	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVV225XKB	123111385	155952079	155952079	123111385	100	61551693	0.0003383	1.00	54.53868	45.87263	35772048	0.283807	0.0020836	32840694	99.99350	100	37689921	91.00	56974263	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVW680LPK	118581069	153225477	153225477	118581069	100	59284066	0.0003044	0.99	55.01467	45.87971	35153671	0.262525	0.0018957	34644408	99.98909	100	38389290	89.49	54123971	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVW999FP9	122111979	175530863	175530863	122111979	100	61050651	0.0000599	1.00	48.28043	41.87448	36754568	0.275443	0.0018434	53418884	99.99126	100	39758243	87.43	54642824	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUVX902YNL	105687552	141270293	141270293	105687552	100	52838977	0.0003394	0.95	55.41355	31.70045	22393705	0.231272	0.0019910	35582741	99.99092	100	24062627	89.75	48398706	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWD538KT3	93128892	129580487	129580487	93128892	100	46561423	0.0001520	0.97	55.12257	46.72140	30272812	0.202011	0.0025389	36451595	99.99351	100	32314676	89.32	42289028	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWD946RDA	149520819	197641724	197641724	149520819	100	74753779	0.0002987	0.96	49.86001	43.02003	42517032	0.316072	0.0020719	48120905	99.99113	100	45622870	88.81	68185631	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWH380YHV	118758017	154302029	154302029	118758017	100	59375307	0.0002332	0.99	56.59547	42.23046	32583607	0.238610	0.0018427	35544012	99.99377	100	34472568	90.88	54730470	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWH955FJF	130639547	170232499	170232499	130639547	100	65312616	0.0001261	1.01	51.82487	39.11938	33300864	0.300246	0.0022484	39592952	99.98904	100	36381430	89.03	59642239	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWJ389FC7	120192862	150666058	150666058	120192862	100	60092014	0.0000771	0.99	57.07302	43.05931	32440780	0.260635	0.0019176	30473196	99.99265	100	34827714	90.90	55551131	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWM344ZLM	117831195	162934462	162934462	117831195	100	58912499	0.0002679	0.99	47.54644	36.20085	29493516	0.317124	0.0020166	45103267	99.99474	100	33397586	87.79	52677231	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWP426NBR	104117727	136600495	136600495	104117727	100	52055846	0.0001242	0.95	60.07319	40.07443	27372491	0.182672	0.0026510	32482768	99.99420	100	28549535	90.96	48071230	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWX167DAH	123682005	192704366	192704366	123682005	100	61834940	0.0001177	1.00	43.57415	37.02141	35674317	0.289182	0.0018338	69022361	99.99020	100	39765447	85.55	54107517	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWY079WUH	129106543	181255681	181255681	129106543	100	64541424	0.0003487	0.98	40.01595	37.65129	34129175	0.412852	0.0023745	52149138	99.98165	100	36559926	87.00	58040835	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUWZ614ARQ	106843000	145508107	145508107	106843000	100	53419244	0.0002842	0.99	47.92555	42.08033	30616507	0.320886	0.0020071	38665107	99.99578	100	33688160	88.80	48202453	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXD985ZU1	140301006	196956825	196956825	140301006	100	70146701	0.0000676	0.99	45.17465	36.03483	35488642	0.339938	0.0021713	56655819	99.99458	100	38729715	87.42	62695888	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXE491RMM	97865811	118906208	118906208	97865811	100	48930212	0.0002695	0.98	66.82962	45.56580	27091815	0.161633	0.0026411	21040397	99.99450	100	28413979	92.38	45870390	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXG265ME9	129621756	168423467	168423467	129621756	100	64806369	0.0005600	1.00	53.74925	41.77200	35179399	0.275283	0.0019760	38801711	99.99304	100	37190260	90.24	59421241	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXH833LL4	142418106	190308209	190308209	142418106	100	71203163	0.0004520	1.01	50.06242	45.10139	42919477	0.306045	0.0020634	47890103	99.99173	100	46255615	89.75	65035209	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXP289KRC	137919894	180193491	180193491	137919894	100	68955155	0.0000422	0.98	56.83071	36.80424	33161771	0.230765	0.0020719	42273597	99.99305	100	33565706	91.30	64019350	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXP495XE2	144883140	207898467	207898467	144883140	100	72437782	0.0005885	0.99	46.52462	35.14467	36534422	0.305425	0.0021574	63015327	99.99477	100	38386537	87.90	64915635	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXP595FFP	82882330	112629927	112629927	82882330	100	41439054	0.0004402	0.97	57.41643	43.96293	24758914	0.187966	0.0024695	29747597	99.99491	100	26423196	90.13	37877172	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXV122FN3	128046620	164194973	164194973	128046620	100	64017537	0.0001862	1.00	55.16521	46.44593	38134683	0.267302	0.0018444	36148353	99.99098	100	41583014	89.72	58733300	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUXX361RUG	107229021	133348579	133348579	107229021	100	53611368	0.0003016	0.99	63.68358	48.23219	32160375	0.181221	0.0026846	26119558	99.99414	100	33003046	92.07	50204894	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYC055XPZ	138951866	173601788	173601788	138951866	100	69470318	0.0001920	0.99	55.76776	40.19634	34893729	0.279873	0.0020410	34649922	99.99192	100	37040582	91.22	64543705	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYC303AJY	120708861	161874054	161874054	120708861	100	60350667	0.0004616	0.98	51.12615	39.61285	32063539	0.286988	0.0021230	41165193	99.99376	100	34113253	90.06	55283224	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYD306HAB	127940942	182627299	182627299	127940942	100	63946168	0.0002491	1.01	36.74887	40.42930	36932268	0.451589	0.0019820	54686357	99.96201	100	42007862	83.18	56076091	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYG208KVV	124891243	199498682	199498682	124891243	100	62442357	0.0001144	0.99	38.73081	31.53442	31456954	0.351701	0.0021026	74607439	99.99477	100	35299541	84.26	54046799	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYG298CA9	123272477	157809619	157809619	123272477	100	61632259	0.0002451	0.97	53.71753	48.08596	37944789	0.287246	0.0019546	34537142	99.99354	100	41968903	89.21	55941940	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYH924UCE	119170920	163713959	163713959	119170920	100	59578923	0.0002091	1.00	52.69253	39.72040	32517623	0.248715	0.0020415	44543039	99.98903	100	34070517	88.79	54150809	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYJ705VN9	122863974	178270837	178270837	122863974	100	61425993	0.0001050	0.98	44.63852	38.44930	34275732	0.324227	0.0022001	55406863	99.99024	100	37266516	85.92	54518769	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYK029WUU	89122275	114077752	114077752	89122275	100	44558477	0.0000914	0.97	61.38720	46.04638	26265846	0.185776	0.0024906	24955477	99.99403	100	28032018	90.95	41147531	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYL008GM4	111596389	136189939	136189939	111596389	100	55793552	0.0001722	0.97	68.59611	32.41083	22071962	0.135216	0.0028679	24593550	99.99168	100	22785219	92.39	52394355	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYL149PRF	108007117	135498385	135498385	108007117	100	54000728	0.0002878	0.98	61.14424	53.84660	36482547	0.206587	0.0025245	27491268	99.99476	100	38738756	91.11	50062588	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYP226CPW	140904052	200107332	200107332	140904052	100	70445538	0.0001431	1.02	45.97181	39.80486	39830197	0.319377	0.0018772	59203280	99.99079	100	43697397	86.71	62985933	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYP235ZLD	112041837	154018964	154018964	112041837	100	56012285	0.0006468	0.98	53.34704	30.31082	23345849	0.236692	0.0022270	41977127	99.98459	100	24774214	88.37	50797298	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYT193FFG	135937514	167443145	167443145	135937514	100	67965213	0.0002058	0.99	55.17711	45.26622	37899750	0.298018	0.0020057	31505631	99.99479	100	40441406	91.04	62909433	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYY225MNZ	86663158	113081381	113081381	86663158	100	43329287	0.0000491	0.97	61.57635	43.19503	24424016	0.168417	0.0025204	26418223	99.99471	100	25706055	91.35	40143805	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYY614DN8	143420041	207828429	207828429	143420041	100	71705432	0.0001386	0.98	43.48929	38.17697	39674516	0.341201	0.0021712	64408388	99.99360	100	44205920	85.74	63160903	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUYY878JGP	133161137	172765129	172765129	133161137	100	66576125	0.0004581	0.99	54.69875	45.73749	39512171	0.264335	0.0020122	39603992	99.99333	100	41230805	90.43	61407501	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZD231YZ6	114115577	160409162	160409162	114115577	100	57054121	0.0003026	0.98	37.42191	39.14512	31398709	0.450324	0.0020169	46293585	99.99357	100	35064123	87.49	50905501	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZE432DZM	130181306	183450507	183450507	130181306	100	65085949	0.0000718	0.98	46.85383	39.45448	36192628	0.311264	0.0019646	53269201	99.99277	100	40115753	87.01	57917361	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZF321EW4	137296801	237074262	237074262	137296801	100	68645200	0.0004753	1.01	35.69136	28.75297	34084476	0.352639	0.0019988	99777461	99.99534	100	38615057	83.54	58499666	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZF473UEP	115673202	160994953	160994953	115673202	100	57829951	0.0005352	0.98	47.71084	36.89973	29707207	0.306990	0.0021394	45321751	99.98850	100	33058534	86.18	51678195	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZJ053JGZ	133079937	177519663	177519663	133079937	100	66536354	0.0003317	1.00	49.27551	37.35663	33159728	0.317630	0.0020517	44439726	99.99457	100	36138181	88.41	59979953	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZK054DP5	120214668	154653148	154653148	120214668	100	60103402	0.0004124	1.04	52.53178	45.78244	35404472	0.298436	0.0018783	34438480	99.99346	100	38496742	89.95	54950104	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZN836GME	145980665	199472112	199472112	145980665	100	72983931	0.0002882	1.01	52.13303	42.78780	42678756	0.260984	0.0020023	53491447	99.99123	100	44497522	89.27	66523707	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZN936HJ9	81372630	106601993	106601993	81372630	100	40681058	0.0003806	1.00	55.49972	40.91089	21809049	0.244893	0.0018392	25229363	99.98708	100	23946737	86.35	37033610	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZP278MR4	131323891	176068176	176068176	131323891	100	65655018	0.0006721	1.01	51.81335	37.00994	32585406	0.279093	0.0019754	44744285	99.98945	100	35651501	88.06	59272066	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZT557DHF	106461904	143299163	143299163	106461904	100	53227723	0.0003853	0.97	58.32994	40.20927	28811446	0.184961	0.0026631	36837259	99.99393	100	30130126	90.24	48805126	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZT902WVB	148124441	182236026	182236026	148124441	100	74058202	0.0000503	0.98	57.46045	43.65235	39777357	0.269224	0.0021408	34111585	99.99457	100	42140814	91.69	68930822	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZV656DD1	148595712	191967771	191967771	148595712	100	74290018	0.0002922	1.01	53.56322	40.64046	39012951	0.283583	0.0019968	43372059	99.98945	100	42775759	89.23	67818461	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZW701NNF	103881710	161910752	161910752	103881710	100	51938334	0.0004089	0.99	38.59967	33.83292	27390995	0.370488	0.0018256	58029042	99.99515	100	31808231	84.18	44505268	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZX521TKK	98509768	147866623	147866623	98509768	100	49251743	0.0011162	0.99	49.59044	37.31938	27593127	0.221318	0.0025534	49356855	99.99362	100	30499773	86.53	43500814	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZX847VWV	119842527	151675489	151675489	119842527	100	59914634	0.0005850	0.99	57.32521	42.14669	31967012	0.249421	0.0019800	31832962	99.98894	100	34686632	89.97	55085136	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZY128BJ2	150783455	204326818	204326818	150783455	100	75386092	0.0001938	0.96	48.60244	37.88189	38704461	0.315447	0.0020149	53543363	99.99253	100	42610444	88.01	67775270	NA	NA	NA	NA	NA	NA
AnswerALS	CASE_NEUZY975XKL	109304246	144951033	144951033	109304246	100	54649315	0.0001080	1.02	50.04858	47.28401	34271213	0.310375	0.0018150	35646787	99.99486	100	38548384	88.36	48940600	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUAA485DZL	142730071	206651342	206651342	142730071	100	71358075	0.0001363	1.01	42.96172	40.46539	41815801	0.350993	0.0019086	63921271	99.99025	100	46974414	85.30	62633765	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUAJ025JC3	95976943	127242318	127242318	95976943	100	47985999	0.0002535	0.98	59.67276	40.91501	26031923	0.178385	0.0026401	31265375	99.99485	100	27673100	90.71	44173605	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUAJ928PAA	119849155	148067308	148067308	119849155	100	59920487	0.0000620	0.98	63.17580	50.11523	37104650	0.193182	0.0026209	28218153	99.99317	100	39200380	91.47	55771640	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUCA748GF2	107664405	137518200	137518200	107664405	100	53827862	0.0002251	0.98	57.66832	32.94083	22651817	0.238273	0.0020644	29853795	99.99194	100	24571396	89.73	49288757	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUCV136DHM	133777770	169397330	169397330	133777770	100	66882436	0.0000651	0.99	55.08695	48.92659	41444984	0.278311	0.0018345	35619560	99.99036	100	45549599	89.72	61182809	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUCV809LL4	75164929	112702935	112702935	75164929	100	37579947	0.0003591	0.99	51.05006	34.10042	19217322	0.199274	0.0029202	37538006	99.99330	100	20568369	87.18	33519005	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUDA782GW3	84711501	107695370	107695370	84711501	100	42353186	0.0000815	1.00	63.74855	38.74052	20862147	0.160241	0.0026666	22983869	99.99395	100	21427666	91.81	39438521	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUDE949BP3	106950527	160325830	160325830	106950527	100	53472417	0.0004657	0.97	50.28890	37.22890	29845269	0.213953	0.0025578	53375303	99.99468	100	31526501	88.57	48108748	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUDM126GNG	109647418	144319019	144319019	109647418	100	54820128	0.0000840	0.98	59.50635	44.56285	32158364	0.185721	0.0027073	34671601	99.99347	100	34382218	89.76	50168400	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUDT762KUL	104193773	168014070	168014070	104193773	100	52094773	0.0003644	1.00	39.04926	32.66405	27441220	0.338047	0.0021123	63820297	99.99594	100	30288348	85.30	45243066	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUEB210XRC	126699869	166317212	166317212	126699869	100	63340865	0.0003199	1.00	48.59671	45.47978	37826434	0.338585	0.0019693	39617343	99.98568	100	42145092	87.81	57006910	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUEY565NWT	99688142	135142105	135142105	99688142	100	49840653	0.0002137	1.00	58.78130	40.86577	27615249	0.170502	0.0026984	35453963	99.99314	100	29065895	90.01	45685875	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUFL733GX5	123100513	163533801	163533801	123100513	100	61545257	0.0002462	1.02	55.30460	38.73854	31677879	0.236233	0.0020375	40433288	99.99188	100	32733496	90.31	56609176	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUFZ500KDB	105364734	144983815	144983815	105364734	100	52678661	0.0001249	0.99	56.25394	40.86537	29626090	0.192852	0.0028539	39619081	99.99297	100	31637441	89.34	47960440	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUFZ508VBV	92018121	113000997	113000997	92018121	100	46006716	0.0000357	1.01	64.99242	44.63934	25222765	0.175065	0.0025146	20982876	99.99490	100	26953022	92.14	42988984	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUHE723FGT	125537737	162056376	162056376	125537737	100	62764270	0.0011938	0.98	58.65879	32.97615	26721907	0.215906	0.0021614	36518639	99.99267	100	26793823	90.97	58252831	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUHZ716BZ2	85710543	111187686	111187686	85710543	100	42852487	0.0002070	0.96	61.79334	39.97116	22222904	0.169172	0.0028450	25477143	99.99350	100	23292684	90.31	39527760	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUJH290RH7	82173096	118342717	118342717	82173096	100	41084532	0.0001731	0.99	54.19480	36.11641	21371505	0.186395	0.0025146	36169621	99.99509	100	23245087	88.94	37082361	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUJX341NDP	86296043	112040549	112040549	86296043	100	43145527	0.0001699	0.95	61.72160	36.76733	20598281	0.169698	0.0026220	25744506	99.99422	100	21891892	90.82	39861968	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUKW131XJ2	95809608	136890063	136890063	95809608	100	47902177	0.0004480	0.97	52.02433	41.41099	28345282	0.226584	0.0025512	41080455	99.99452	100	30623541	88.47	43164946	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEULL933JXY	110585326	143995298	143995298	110585326	100	55288588	0.0000544	0.99	55.48995	40.87436	29430905	0.252399	0.0018215	33409972	99.99263	100	32283777	89.42	50400099	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUMA002VLD	135552971	169095441	169095441	135552971	100	67772754	0.0000385	0.98	53.41844	46.03283	38922106	0.310142	0.0020246	33542470	99.99449	100	41089506	91.08	62765223	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUMF089KLV	117156561	165059662	165059662	117156561	100	58566711	0.0001651	0.98	44.88286	38.14853	31490598	0.341550	0.0020028	47903101	99.98025	100	35167692	85.93	52245074	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUML507PFJ	112923055	150315261	150315261	112923055	100	56449107	0.0001161	1.02	43.60568	44.67974	33588188	0.396560	0.0020184	37392206	99.97800	100	37457697	87.15	51219941	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUMN061ATZ	93524847	128173953	128173953	93524847	100	46759563	0.0001344	0.99	57.80673	45.27378	29016282	0.175560	0.0027322	34649106	99.99388	100	29752572	90.24	43033290	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUMT184NWC	136862206	224271425	224271425	136862206	100	68422512	0.0025125	0.99	39.43972	32.22339	36139122	0.321582	0.0021129	87409219	99.98745	100	41155454	82.33	58323568	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUNC876ZB2	118137032	152219678	152219678	118137032	100	59063901	0.0001150	1.00	52.67947	45.68107	34770809	0.295167	0.0018412	34082646	99.99219	100	38077080	88.79	53739361	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUNN472ACB	115095631	163191184	163191184	115095631	100	57541164	0.0002525	1.01	45.84206	40.27677	32868036	0.322258	0.0022235	48095553	99.98844	100	37297185	86.51	50810753	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUNW343RXP	81656013	101975419	101975419	81656013	100	40825164	0.0000734	0.99	63.94251	45.41374	23157025	0.172710	0.0026231	20319406	99.99304	100	24466778	91.80	38038971	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUPH301NNX	97626796	124778743	124778743	97626796	100	48810411	0.0007084	0.98	62.90073	38.68959	24139662	0.168067	0.0026556	27151947	99.99388	100	25335234	91.23	45245936	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUPL878MTL	119315528	145479308	145479308	119315528	100	59652672	0.0001063	1.01	59.15472	45.27052	32932752	0.255547	0.0018693	26163780	99.99146	100	35298095	91.07	55420022	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUPW536ZKZ	140584593	183287662	183287662	140584593	100	70282990	0.0000454	1.00	47.46122	45.68001	41869158	0.357446	0.0019376	42703069	99.98676	100	47060687	88.27	63578832	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEURJ861MMD	126644009	177617449	177617449	126644009	100	63318324	0.0001233	0.99	54.49429	33.77473	29996606	0.204296	0.0026134	50973440	99.99419	100	32347065	88.58	57183408	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEURV546WMW	157220261	202295873	202295873	157220261	100	78604322	0.0002336	1.01	53.00219	40.20670	40671295	0.293329	0.0021206	45075612	99.99261	100	42355896	90.81	72498559	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUUV825HYF	83800552	107396217	107396217	83800552	100	41897686	0.0004498	0.96	63.56130	37.26202	20010218	0.157226	0.0026666	23595665	99.99382	100	20854070	91.47	38901768	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUVZ050YX7	92660498	126950374	126950374	92660498	100	46327705	0.0003695	0.96	58.44763	35.38709	22463170	0.166282	0.0026063	34289876	99.99451	100	23548444	89.93	42302176	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUWN092BVG	124441297	267096673	267096673	124441297	100	62217948	0.0007366	1.02	26.44413	22.36445	29868384	0.399273	0.0018759	142655376	99.99566	100	35643330	77.13	49313107	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUWT164JRQ	135918939	165861184	165861184	135918939	100	67954059	0.0006845	0.99	60.66825	36.63712	30385906	0.236310	0.0021812	29942245	99.99204	100	31316871	92.30	63842878	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUXC258VTR	152107663	209900868	209900868	152107663	100	76050099	0.0001636	1.00	47.44388	37.26139	39107873	0.318962	0.0022160	57793205	99.99509	100	42315109	88.66	68669786	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUXP955XW7	114681956	149912733	149912733	114681956	100	57335068	0.0001184	1.01	52.71462	39.41866	29550314	0.283886	0.0018471	35230777	99.98969	100	32850947	88.44	51944509	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUXW311EFC	104639552	288942845	288942845	104639552	100	52317273	0.0001632	1.02	18.01321	13.99294	20216523	0.464670	0.0020450	184303293	99.99522	100	25421145	69.72	37720814	NA	NA	NA	NA	NA	NA
AnswerALS	CTRL_NEUYM205MRL	107448896	130702708	130702708	107448896	100	53721197	0.0001384	0.98	66.54306	44.21693	28898107	0.163942	0.0026897	23253812	99.99395	100	30061334	92.29	50334794	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072001A02	135941676	230048169	230048169	135941676	100	67891519	0.0000486	1.00	38.23806	NA	NA	0.322099	0.0044128	94106493	99.88330	NA	NA	85.10	59399312	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072001B02	94178800	113979200	113979200	94178800	100	47033246	0.0002407	1.04	58.12804	NA	NA	0.270977	0.0041548	19800400	99.88075	NA	NA	91.78	44306370	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072002A02	128354706	233021285	233021285	128354706	100	64131194	0.0000189	1.05	32.35120	NA	NA	0.385579	0.0035951	104666579	99.92808	NA	NA	81.85	54374177	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072002B02	121345546	178706446	178706446	121345546	100	60617500	0.0000132	1.03	43.85413	NA	NA	0.325116	0.0033535	57360900	99.90890	NA	NA	83.17	54504534	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072006A01	127718938	173144213	173144213	127718938	100	63815376	0.0001075	1.08	48.64651	NA	NA	0.314414	0.0034966	45425275	99.93095	NA	NA	89.19	58172615	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072006B01	126436139	163172628	163172628	126436139	100	63166742	0.0000985	1.04	52.35554	NA	NA	0.298745	0.0032790	36736489	99.91881	NA	NA	89.75	58149679	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072007A01	125824321	159464428	159464428	125824321	100	62865712	0.0000072	1.09	52.17988	NA	NA	0.313698	0.0036019	33640107	99.92617	NA	NA	90.13	58022536	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072007B01	140248486	185851687	185851687	140248486	100	70064449	0.0000110	1.02	49.51831	NA	NA	0.317949	0.0033093	45603201	99.91473	NA	NA	88.78	64085726	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072008A02	113439206	174996013	174996013	113439206	100	56644047	0.0001302	1.00	44.07174	NA	NA	0.287272	0.0049033	61556807	99.86679	NA	NA	86.51	50470377	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072008B02	130419423	186533158	186533158	130419423	100	65118457	0.0001133	1.02	48.09248	NA	NA	0.282421	0.0047360	56113735	99.86006	NA	NA	88.34	59327132	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072010A02	97616064	123704269	123704269	97616064	100	48751803	0.0002113	1.02	56.76044	NA	NA	0.253716	0.0043931	26088205	99.88480	NA	NA	90.40	45386503	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072010B02	97718802	128795458	128795458	97718802	100	48795660	0.0002677	1.02	53.05946	NA	NA	0.271663	0.0043221	31076656	99.86954	NA	NA	89.62	45162304	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072012A01	148024478	221266815	221266815	148024478	100	73944529	0.0000147	1.06	41.98420	NA	NA	0.345136	0.0035806	73242337	99.90852	NA	NA	85.59	65569118	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072012B01	122573980	213140649	213140649	122573980	100	61231109	0.0000237	1.09	34.86024	NA	NA	0.363857	0.0034863	90566669	99.90882	NA	NA	82.91	52372164	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072013A02	118696846	192328501	192328501	118696846	100	59305314	0.0000342	1.07	38.34418	NA	NA	0.350213	0.0035889	73631655	99.92736	NA	NA	85.32	51716157	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072013B02	46670716	59683321	59683321	46670716	100	23314228	0.0000345	1.02	56.50135	NA	NA	0.246293	0.0037340	13012605	99.90945	NA	NA	90.82	21658777	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072014A02	126791091	241860665	241860665	126791091	100	63323993	0.0000448	0.97	32.89437	NA	NA	0.338306	0.0042676	115069574	99.88713	NA	NA	82.07	53450807	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072014B02	128538219	181437080	181437080	128538219	100	64204227	0.0000319	1.02	48.77057	NA	NA	0.282723	0.0038709	52898861	99.89905	NA	NA	89.19	58677514	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072015A01	115356666	158112293	158112293	115356666	100	57615661	0.0001570	1.04	48.97028	NA	NA	0.300918	0.0039417	42755627	99.89134	NA	NA	88.68	52283322	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072015B01	126695445	219773032	219773032	126695445	100	63292889	0.0006390	1.05	35.27499	NA	NA	0.357848	0.0034305	93077587	99.91344	NA	NA	83.83	54369447	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072018A02	111320345	138933136	138933136	111320345	100	55562883	0.0001702	1.06	54.60476	NA	NA	0.291659	0.0040284	27612791	99.82521	NA	NA	88.21	51515998	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072018B02	132755451	180480035	180480035	132755451	100	66288152	0.0001320	1.01	49.23297	NA	NA	0.304696	0.0040931	47724584	99.86505	NA	NA	88.72	60940845	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072019A02	124986603	236421103	236421103	124986603	100	62440538	0.0001764	1.02	32.79879	NA	NA	0.347422	0.0038855	111434500	99.91557	NA	NA	82.54	52805605	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072019B02	147282515	183896260	183896260	147282515	100	73550040	0.0001682	0.98	53.82492	NA	NA	0.303372	0.0040621	36613745	99.87613	NA	NA	90.94	68691397	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072028A01	132870476	220521382	220521382	132870476	100	66373545	0.0001004	1.07	37.28181	NA	NA	0.351354	0.0036057	87650906	99.90714	NA	NA	82.84	57550940	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072028B01	128995074	193530490	193530490	128995074	100	64452299	0.0001071	1.06	41.89889	NA	NA	0.343485	0.0031821	64535416	99.92986	NA	NA	85.95	57436868	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072029A01	106521084	182347069	182347069	106521084	100	53202122	0.0003117	1.06	36.33133	NA	NA	0.346029	0.0039574	75825985	99.89031	NA	NA	83.28	45652536	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072029B01	129663114	155124570	155124570	129663114	100	64781383	0.0000279	1.10	55.16994	NA	NA	0.316344	0.0031647	25461456	99.92261	NA	NA	90.69	60478486	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072034A01	126821822	169942398	169942398	126821822	100	63361107	0.0000734	1.05	49.69402	NA	NA	0.307243	0.0036640	43120576	99.92146	NA	NA	88.71	58025659	NA	NA	NA	NA	NA	NA
neurolincs.diMN	00072034C01	136723117	187549403	187549403	136723117	100	68306236	0.0001140	1.04	45.57472	NA	NA	0.349683	0.0032756	50826286	99.91907	NA	NA	87.16	62019587	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-00iCTR-003	72933637	115482294	115482294	72933637	100	36430618	0.0000614	1.03	48.36477	NA	NA	0.196205	0.0021612	42548657	99.90073	NA	NA	86.39	32117381	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-00iCTR-004	80664165	114902116	114902116	80664165	100	40291268	0.0000522	1.06	53.36115	NA	NA	0.205768	0.0019302	34237951	99.89880	NA	NA	87.58	36178657	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-25iCTR-003	90791001	196170471	196170471	90791001	100	45356754	0.0001678	1.04	29.61257	NA	NA	0.321581	0.0020212	105379470	99.91465	NA	NA	76.83	35959903	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-25iCTR-004	105034279	152195347	152195347	105034279	100	52463612	0.0000295	1.08	50.06550	NA	NA	0.243061	0.0017331	47161068	99.89808	NA	NA	85.75	46397163	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-28iALS-003	60575786	85175631	85175631	60575786	100	30261072	0.0000304	1.00	56.65664	NA	NA	0.169235	0.0019201	24599845	99.91145	NA	NA	89.22	27509794	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-28iALS-005	85676346	138127203	138127203	85676346	100	42771822	0.0000311	1.02	46.50457	NA	NA	0.215862	0.0017702	52450857	99.84511	NA	NA	85.96	37588074	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-29iALS-003	87345844	104514733	104514733	87345844	100	43633538	0.0000234	1.03	62.47783	NA	NA	0.228698	0.0018449	17168889	99.90982	NA	NA	90.52	40374838	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-29iALS-004	95816596	141144444	141144444	95816596	100	47865904	0.0000585	1.05	48.69636	NA	NA	0.251449	0.0017006	45327848	99.91151	NA	NA	86.92	42550998	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-30iALS-003	77416918	102396365	102396365	77416918	100	38671139	0.0000805	1.04	58.61526	NA	NA	0.194683	0.0019603	24979447	99.90359	NA	NA	88.96	35212928	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-30iALS-004	102751248	136491201	136491201	102751248	100	51326745	0.0000490	1.07	58.26979	NA	NA	0.197065	0.0017537	33739953	99.90486	NA	NA	89.08	46825808	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-52iALS-003	73314114	105152444	105152444	73314114	100	36626533	0.0000241	1.02	49.57568	NA	NA	0.256968	0.0018323	31838330	99.91673	NA	NA	87.63	32786448	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-52iALS-004	95698993	133431493	133431493	95698993	100	47804764	0.0000155	1.07	50.82951	NA	NA	0.262022	0.0016450	37732500	99.90651	NA	NA	87.51	43059847	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-83iCTR-003	95760241	243258163	243258163	95760241	100	47840562	0.0000123	1.08	22.95447	NA	NA	0.376408	0.0020284	147497922	99.91738	NA	NA	71.68	35437258	NA	NA	NA	NA	NA	NA
neurolincs.diMN	A-042-83iCTR-004	84808205	166729922	166729922	84808205	100	42367425	0.0000080	1.09	33.60215	NA	NA	0.301175	0.0017554	81921717	99.91350	NA	NA	79.32	34527944	NA	NA	NA	NA	NA	NA
catanese	c9orf72_1	75957394	81967185	81967185	75957394	100	37968138	0.0000180	1.08	61.65157	NA	NA	0.315076	0.0025560	6009791	99.97220	NA	NA	95.02	36788530	NA	NA	NA	NA	NA	NA
catanese	c9orf72_2	72919132	78480260	78480260	72919132	100	36451110	0.0000282	1.05	62.35228	NA	NA	0.309170	0.0026208	5561128	99.97681	NA	NA	95.08	35311214	NA	NA	NA	NA	NA	NA
catanese	c9orf72_3	76337728	82563723	82563723	76337728	100	38161015	0.0000060	1.06	58.64808	NA	NA	0.346512	0.0027519	6225995	99.97944	NA	NA	94.71	36947989	NA	NA	NA	NA	NA	NA
catanese	c9orf72_4	71229641	76888537	76888537	71229641	100	35607323	0.0000226	1.10	60.84190	NA	NA	0.323337	0.0025268	5658896	99.97895	NA	NA	94.78	34466646	NA	NA	NA	NA	NA	NA
catanese	c9orf72_5	70109568	76105593	76105593	70109568	100	35046568	0.0000163	1.09	56.96976	NA	NA	0.362158	0.0026023	5996025	99.97656	NA	NA	94.61	33883013	NA	NA	NA	NA	NA	NA
catanese	c9orf72_6	69814167	75301066	75301066	69814167	100	34898923	0.0000098	1.11	57.44992	NA	NA	0.361781	0.0026903	5486899	99.97662	NA	NA	94.95	33801000	NA	NA	NA	NA	NA	NA
catanese	ctrl_1	65434941	70580531	70580531	65434941	100	32708636	0.0000245	1.08	59.90526	NA	NA	0.334629	0.0025768	5145590	99.97300	NA	NA	95.09	31699462	NA	NA	NA	NA	NA	NA
catanese	ctrl_2	60047749	64571298	64571298	60047749	100	30017201	0.0000076	1.06	62.14138	NA	NA	0.312248	0.0023685	4523549	99.97777	NA	NA	95.42	29103408	NA	NA	NA	NA	NA	NA
catanese	ctrl_3	63620482	68216444	68216444	63620482	100	31804721	0.0000107	1.08	59.72607	NA	NA	0.341274	0.0024669	4595962	99.98265	NA	NA	95.50	30862009	NA	NA	NA	NA	NA	NA
catanese	fus_1	67955571	73428734	73428734	67955571	100	33970617	0.0000100	1.06	60.63928	NA	NA	0.325379	0.0025217	5473163	99.97890	NA	NA	95.00	32894443	NA	NA	NA	NA	NA	NA
catanese	fus_2	63220005	68675328	68675328	63220005	100	31603980	0.0000072	1.07	60.85049	NA	NA	0.319067	0.0025170	5455323	99.98095	NA	NA	95.21	30591145	NA	NA	NA	NA	NA	NA
catanese	fus_3	74148845	79882326	79882326	74148845	100	37066760	0.0000092	1.05	57.39093	NA	NA	0.363480	0.0025698	5733481	99.97933	NA	NA	95.30	35918835	NA	NA	NA	NA	NA	NA
catanese	fus_4	59851095	64881696	64881696	59851095	100	29921067	0.0000190	1.07	61.06491	NA	NA	0.318017	0.0025564	5030601	99.98503	NA	NA	95.41	28970978	NA	NA	NA	NA	NA	NA
catanese	fus_5	70100137	75733720	75733720	70100137	100	35043505	0.0000162	1.06	55.75257	NA	NA	0.379645	0.0024940	5633583	99.98127	NA	NA	95.09	33946048	NA	NA	NA	NA	NA	NA
catanese	fus_6	66401477	72139932	72139932	66401477	100	33195335	0.0000102	1.08	58.00465	NA	NA	0.350565	0.0025423	5738455	99.98372	NA	NA	94.95	32122277	NA	NA	NA	NA	NA	NA
catanese	iso_1	65420693	70669639	70669639	65420693	100	32703372	0.0000000	1.06	60.57990	NA	NA	0.326263	0.0027316	5248946	99.97868	NA	NA	95.13	31687063	NA	NA	NA	NA	NA	NA
catanese	iso_2	72233630	78605662	78605662	72233630	100	36107695	0.0000000	1.05	58.27189	NA	NA	0.346863	0.0024793	6372032	99.97475	NA	NA	95.10	34960517	NA	NA	NA	NA	NA	NA
catanese	iso_3	70716047	76451317	76451317	70716047	100	35350396	0.0000065	1.04	61.47153	NA	NA	0.316114	0.0024646	5735270	99.97843	NA	NA	95.15	34278261	NA	NA	NA	NA	NA	NA
dafinca	c9orf72_1	121035567	132747772	132747772	121035567	100	60511122	0.0000018	1.19	58.86387	NA	NA	0.331559	0.0026354	11712205	99.98899	NA	NA	92.58	57798843	NA	NA	NA	NA	NA	NA
dafinca	c9orf72_2	118789660	132869385	132869385	118789660	100	59388555	0.0000038	1.31	65.47521	NA	NA	0.238722	0.0023471	14079725	99.98944	NA	NA	91.76	56299561	NA	NA	NA	NA	NA	NA
dafinca	c9orf72_3	101537136	109650109	109650109	101537136	100	50761452	0.0000000	1.14	65.64582	NA	NA	0.265317	0.0024822	8112973	99.98598	NA	NA	91.22	48515807	NA	NA	NA	NA	NA	NA
dafinca	c9orf72_4	106049359	119503299	119503299	106049359	100	53018709	0.0000000	1.21	62.38078	NA	NA	0.269820	0.0024909	13453940	99.98874	NA	NA	92.11	50254110	NA	NA	NA	NA	NA	NA
dafinca	ctrl_1	105491420	119502002	119502002	105491420	100	52737233	0.0000021	1.22	67.63313	NA	NA	0.203468	0.0027350	14010582	99.98393	NA	NA	91.40	50043374	NA	NA	NA	NA	NA	NA
dafinca	iso_1	110514258	126081076	126081076	110514258	100	55250944	0.0000020	1.14	58.38462	NA	NA	0.305962	0.0025204	15566818	99.98881	NA	NA	89.66	51904662	NA	NA	NA	NA	NA	NA
dafinca	iso_2	106736217	117587500	117587500	106736217	100	53359671	0.0000000	1.16	59.85868	NA	NA	0.315709	0.0026161	10851283	99.98419	NA	NA	90.48	50824778	NA	NA	NA	NA	NA	NA
dafinca	iso_3	106149403	119518192	119518192	106149403	100	53067334	0.0000063	1.19	67.64927	NA	NA	0.208851	0.0026364	13368789	99.98612	NA	NA	90.97	50439866	NA	NA	NA	NA	NA	NA
dafinca	iso_4	92324252	103350221	103350221	92324252	100	46155034	0.0000000	1.18	57.64835	NA	NA	0.329921	0.0026080	11025969	99.98464	NA	NA	89.83	43738930	NA	NA	NA	NA	NA	NA
dafinca	iso_5	110135429	123636396	123636396	110135429	100	55060726	0.0000000	1.07	50.65312	NA	NA	0.408146	0.0024266	13500967	99.98731	NA	NA	89.57	51988008	NA	NA	NA	NA	NA	NA
dafinca	iso_6	112546857	126042797	126042797	112546857	100	56265174	0.0000000	1.23	45.18061	NA	NA	0.474039	0.0025985	13495940	99.98533	NA	NA	89.66	53279237	NA	NA	NA	NA	NA	NA
dafinca	iso_7	94610729	105135911	105135911	94610729	100	47299602	0.0000024	1.23	59.79154	NA	NA	0.310400	0.0024351	10525182	99.98782	NA	NA	90.88	44856979	NA	NA	NA	NA	NA	NA
dafinca	ctrl_1	16576302	17489968	17489968	16576302	100	8275371	0.0000000	1.08	85.36618	NA	NA	0.073477	0.0041740	913666	99.84580	NA	NA	96.02	8070745	NA	NA	NA	NA	NA	NA
dafinca	ctrl_2	18972276	20097878	20097878	18972276	100	9472448	0.0000000	1.09	83.99444	NA	NA	0.082375	0.0040685	1125602	99.85568	NA	NA	95.60	9202716	NA	NA	NA	NA	NA	NA
dafinca	ctrl_3	19783273	20867596	20867596	19783273	100	9878007	0.0000000	1.11	84.84853	NA	NA	0.079675	0.0039749	1084323	99.86221	NA	NA	96.04	9633247	NA	NA	NA	NA	NA	NA
dafinca	ctrl_4	15583580	16625552	16625552	15583580	100	7776614	0.0000000	1.21	81.17492	NA	NA	0.106605	0.0039203	1041972	99.80523	NA	NA	91.17	7568676	NA	NA	NA	NA	NA	NA
dafinca	tardbp_1	19574454	20693487	20693487	19574454	100	9772054	0.0000000	1.21	83.90709	NA	NA	0.086220	0.0038139	1119033	99.84497	NA	NA	94.26	9511682	NA	NA	NA	NA	NA	NA
dafinca	tardbp_2	18517769	19719622	19719622	18517769	100	9239181	0.0000372	1.23	82.91080	NA	NA	0.089737	0.0041516	1201853	99.78719	NA	NA	93.02	8998264	NA	NA	NA	NA	NA	NA
dafinca	tardbp_3	20485715	21679042	21679042	20485715	100	10224310	0.0000000	1.19	81.68852	NA	NA	0.109326	0.0039982	1193327	99.81892	NA	NA	93.58	9957003	NA	NA	NA	NA	NA	NA
dafinca	tardbp_4	21895246	23787368	23787368	21895246	100	10932302	0.0000211	1.29	71.93412	NA	NA	0.191469	0.0039524	1892122	99.86005	NA	NA	93.74	10582849	NA	NA	NA	NA	NA	NA
dafinca	tardbp_5	18544776	19538517	19538517	18544776	100	9258793	0.0000129	1.09	84.43084	NA	NA	0.083507	0.0040231	993741	99.85338	NA	NA	95.57	9003671	NA	NA	NA	NA	NA	NA
dafinca	tardbp_6	20071514	21044889	21044889	20071514	100	10025089	0.0000118	1.09	85.35948	NA	NA	0.080760	0.0036381	973375	99.89370	NA	NA	96.13	9778365	NA	NA	NA	NA	NA	NA
luisier	d35_ctrl_1	14137164	17365755	17365755	14137164	100	14137164	0.0000319	0.97	NA	NA	NA	0.424189	0.0025543	3228591	0.00000	NA	NA	89.92	12777849	1.9300484	NA	47	60.00000	35.22582	47
luisier	d35_ctrl_2	12395390	15087201	15087201	12395390	100	12395390	0.0000000	0.92	NA	NA	NA	0.435478	0.0028154	2691811	0.00000	NA	NA	90.20	11235044	1.9136214	NA	47	60.00000	36.35613	47
luisier	d35_ctrl_3	13781703	16430800	16430800	13781703	100	13781703	0.0000000	0.92	NA	NA	NA	0.455100	0.0027615	2649097	0.00000	NA	NA	90.76	12561469	1.8540827	NA	47	60.00000	37.38918	47
luisier	d35_vcp_1	10394568	12882428	12882428	10394568	100	10394568	0.0000135	1.09	NA	NA	NA	0.446962	0.0024339	2487860	0.00000	NA	NA	89.00	9302422	2.0395963	NA	48	60.00000	37.34052	48
luisier	d35_vcp_2	15815865	19279401	19279401	15815865	100	15815865	0.0000000	1.00	NA	NA	NA	0.443607	0.0024008	3463536	0.00000	NA	NA	90.36	14356502	2.0067293	NA	48	60.00000	36.71011	48
luisier	d35_vcp_3	5906382	7352632	7352632	5906382	100	5906382	0.0000000	0.87	NA	NA	NA	0.282392	0.0029136	1446250	0.00000	NA	NA	90.28	5362641	1.8340739	NA	45	60.00000	22.58967	45
wang	iso_1	30043364	31484983	31484983	30043364	100	14914560	0.0000161	1.08	77.98233	NA	NA	0.157261	0.0063193	1441619	99.28688	NA	NA	90.82	14677818	NA	NA	NA	NA	NA	NA
wang	iso_2	30198322	31651805	31651805	30198322	100	14981698	0.0000641	1.04	78.00677	NA	NA	0.156546	0.0065433	1453483	99.22206	NA	NA	90.39	14766976	NA	NA	NA	NA	NA	NA
wang	sod1_1	30809361	32337592	32337592	30809361	100	15287653	0.0000315	1.06	78.14520	NA	NA	0.153305	0.0065095	1528231	99.24031	NA	NA	90.32	15039892	NA	NA	NA	NA	NA	NA
wang	sod1_2	30686515	32213431	32213431	30686515	100	15236081	0.0000159	1.05	78.11696	NA	NA	0.154028	0.0062301	1526916	99.30147	NA	NA	90.98	14983631	NA	NA	NA	NA	NA	NA
kiskinis	iso_1	12452702	17772558	17772558	12452702	100	6217630	0.0000000	1.23	55.95839	NA	NA	0.138765	0.0025517	5319856	99.85993	NA	NA	80.22	5657335	NA	NA	NA	NA	NA	NA
kiskinis	iso_2	10126374	14391602	14391602	10126374	100	5057244	0.0000000	1.17	59.25709	NA	NA	0.092385	0.0055493	4265228	99.88262	NA	NA	57.22	4604554	NA	NA	NA	NA	NA	NA
kiskinis	iso_3	18104053	32559601	32559601	18104053	100	9040767	0.0000000	1.21	41.11135	NA	NA	0.188924	0.0029665	14455548	99.87561	NA	NA	72.59	7772222	NA	NA	NA	NA	NA	NA
kiskinis	sod1_1	16718799	18243146	18243146	16718799	100	8343800	0.0000747	1.11	36.75684	NA	NA	0.579065	0.0036592	1524347	99.81339	NA	NA	71.79	8048144	NA	NA	NA	NA	NA	NA
kiskinis	sod1_2	30656110	32740754	32740754	30656110	100	15295018	0.0000000	1.15	39.27142	NA	NA	0.563443	0.0020756	2084644	99.78447	NA	NA	91.61	14850599	NA	NA	NA	NA	NA	NA
sareen	c9orf72_1	24845406	33212470	33212470	24845406	100	24845406	0.0000101	1.09	NA	NA	NA	0.493514	0.0028375	8367064	0.00000	NA	NA	86.58	21655725	1.7767771	NA	50	50.00000	42.08267	50
sareen	c9orf72_2	28151852	37739985	37739985	28151852	100	28151852	0.0000000	1.10	NA	NA	NA	0.513295	0.0028173	9588133	0.00000	NA	NA	86.21	24431401	1.9300992	NA	50	50.00000	43.94880	50
sareen	c9orf72_3	41219527	56126483	56126483	41219527	100	41219527	0.0000099	1.07	NA	NA	NA	0.527217	0.0030292	14906956	0.00000	NA	NA	86.16	35777527	1.7798850	NA	50	50.00000	45.31533	50
sareen	c9orf72_4	36409834	51259702	51259702	36409834	100	36409834	0.0000035	1.09	NA	NA	NA	0.556295	0.0027945	14849868	0.00000	NA	NA	85.25	31216316	1.7837984	NA	49	50.00000	48.03861	50
sareen	ctrl_1	34637930	47037378	47037378	34637930	100	34637930	0.0000113	1.09	NA	NA	NA	0.515683	0.0031012	12399448	0.00000	NA	NA	86.02	29995779	1.7143701	NA	49	50.00000	44.23380	50
sareen	ctrl_2	36036948	51713786	51713786	36036948	100	36036948	0.0000040	1.07	NA	NA	NA	0.529704	0.0030175	15676838	0.00000	NA	NA	83.66	30377803	1.8764297	NA	50	50.00000	45.92756	50
sareen	ctrl_3	30120447	41597088	41597088	30120447	100	30120447	0.0000000	1.10	NA	NA	NA	0.527209	0.0028863	11476641	0.00000	NA	NA	85.80	26005996	1.7897096	NA	50	50.00000	45.40106	50
sareen	ctrl_4	32042851	45335936	45335936	32042851	100	32042851	0.0000000	1.11	NA	NA	NA	0.564093	0.0028951	13293085	0.00000	NA	NA	84.18	27146239	1.8080937	NA	50	50.00000	49.01965	50
sommer	c9orf72_1	64336887	68180133	68180133	64336887	100	32164997	0.0000211	1.15	57.56799	NA	NA	0.371038	0.0035648	3843246	99.98929	NA	NA	95.53	31119676	NA	NA	NA	NA	NA	NA
sommer	c9orf72_2	59830017	63876868	63876868	59830017	100	29911673	0.0000151	1.18	58.66177	NA	NA	0.354318	0.0044798	4046851	99.98885	NA	NA	95.38	28942710	NA	NA	NA	NA	NA	NA
sommer	c9orf72_3	69515736	74358559	74358559	69515736	100	34754477	0.0000065	1.16	53.89325	NA	NA	0.405207	0.0037721	4842823	99.99024	NA	NA	95.36	33598568	NA	NA	NA	NA	NA	NA
sommer	c9orf72_4	80391972	86053600	86053600	80391972	100	40188899	0.0000113	1.19	56.87527	NA	NA	0.371822	0.0037454	5661628	99.98237	NA	NA	95.13	38828950	NA	NA	NA	NA	NA	NA
sommer	c9orf72_5	61652359	65967842	65967842	61652359	100	30821964	0.0000074	1.16	59.42428	NA	NA	0.344064	0.0033644	4315483	99.98632	NA	NA	95.58	29791587	NA	NA	NA	NA	NA	NA
sommer	c9orf72_6	70120140	75192973	75192973	70120140	100	35054981	0.0000227	1.20	59.53601	NA	NA	0.340776	0.0038008	5072833	99.98548	NA	NA	95.07	33842839	NA	NA	NA	NA	NA	NA
sommer	ctrl_1	61955188	66357819	66357819	61955188	100	30973008	0.0000256	1.15	60.87844	NA	NA	0.326305	0.0055210	4402631	99.98520	NA	NA	94.27	29911391	NA	NA	NA	NA	NA	NA
sommer	ctrl_2	70169531	75521771	75521771	70169531	100	35078491	0.0000097	1.13	60.25348	NA	NA	0.330383	0.0048517	5352240	99.98212	NA	NA	94.38	33866702	NA	NA	NA	NA	NA	NA
sommer	ctrl_3	62797464	67487027	67487027	62797464	100	31393786	0.0000327	1.16	61.94428	NA	NA	0.312421	0.0042264	4689563	99.98425	NA	NA	95.09	30310132	NA	NA	NA	NA	NA	NA
sommer	ctrl_4	64222789	69085377	69085377	64222789	100	32105084	0.0000282	1.22	55.42455	NA	NA	0.383816	0.0037653	4862588	99.98035	NA	NA	95.04	30986550	NA	NA	NA	NA	NA	NA
sommer	ctrl_5	62956346	66994033	66994033	62956346	100	31473476	0.0000036	1.21	58.64255	NA	NA	0.356663	0.0042383	4037687	99.98508	NA	NA	95.39	30464986	NA	NA	NA	NA	NA	NA
sommer	ctrl_6	61029668	64804558	64804558	61029668	100	30511929	0.0000185	1.27	55.20029	NA	NA	0.396642	0.0044914	3774890	99.99048	NA	NA	95.64	29601506	NA	NA	NA	NA	NA	NA
sterneckert	c9orf72_1	29486569	33917688	33917688	29486569	100	29486569	0.0000120	0.90	NA	NA	NA	0.579341	0.0027601	4431119	0.00000	NA	NA	92.87	27517196	1.9098705	NA	48	76.00000	47.13294	48
sterneckert	c9orf72_2	31243868	36606014	36606014	31243868	100	31243868	0.0000038	0.93	NA	NA	NA	0.577691	0.0028034	5362146	0.00000	NA	NA	92.55	29058077	1.7791890	NA	48	76.00000	46.60611	48
sterneckert	c9orf72_3	32063553	37667089	37667089	32063553	100	32063553	0.0000148	0.94	NA	NA	NA	0.588367	0.0027117	5603536	0.00000	NA	NA	92.49	29798603	2.0554790	NA	48	76.00000	47.71547	48
sterneckert	ctrl_1	33374081	38505971	38505971	33374081	100	33374081	0.0000071	0.89	NA	NA	NA	0.601435	0.0028147	5131890	0.00000	NA	NA	92.91	31164000	2.0262374	NA	47	76.00000	48.85676	48
sterneckert	ctrl_2	34261753	40216782	40216782	34261753	100	34261753	0.0000103	0.92	NA	NA	NA	0.614326	0.0027964	5955029	0.00000	NA	NA	92.58	31871446	1.9240435	NA	47	76.00000	49.77593	48
sterneckert	ctrl_3	33589817	38967746	38967746	33589817	100	33589817	0.0000140	0.91	NA	NA	NA	0.610028	0.0028401	5377929	0.00000	NA	NA	92.83	31330830	1.6798903	NA	47	76.00000	49.31932	48
kapeli	ctrl_1	20435843	25667654	25667654	20435843	100	20435843	0.0000061	0.85	NA	NA	NA	0.554723	0.0047651	5231811	0.00000	NA	NA	87.77	18036576	2.1085959	NA	48	50.00000	22.71533	48
kapeli	ctrl_2	30183571	37590329	37590329	30183571	100	30183571	0.0000000	0.86	NA	NA	NA	0.582816	0.0034462	7406758	0.00000	NA	NA	86.97	26825417	1.6451473	NA	47	50.00000	49.82654	47
kapeli	ctrl_3	12990116	16093163	16093163	12990116	100	12990116	0.0000000	0.83	NA	NA	NA	0.455431	0.0066942	3103047	0.00000	NA	NA	87.30	11590391	1.6911131	NA	47	50.00000	36.04786	47
kapeli	fus_1	11628347	14571553	14571553	11628347	100	11628347	0.0000000	0.89	NA	NA	NA	0.421617	0.0026919	2943206	0.00000	NA	NA	88.79	10382274	1.6719885	NA	47	50.00000	35.60242	47
kapeli	fus_2	20542668	26014667	26014667	20542668	100	20542668	0.0000130	0.82	NA	NA	NA	0.506807	0.0025970	5471999	0.00000	NA	NA	88.57	18294585	1.7357264	NA	47	50.00000	43.59158	48
kapeli	fus_3	29894560	37829682	37829682	29894560	100	29894560	0.0000089	0.82	NA	NA	NA	0.567029	0.0027094	7935122	0.00000	NA	NA	88.36	26553868	1.6529225	NA	48	50.00000	48.45148	48
desantis	ctrl_1	36464752	66855277	66855277	36464752	100	18210429	0.0000810	1.04	38.58190	NA	NA	0.251628	0.0022052	30390525	99.87963	NA	NA	82.22	15195161	NA	NA	NA	NA	NA	NA
desantis	ctrl_2	40806682	97439508	97439508	40806682	100	20381742	0.0001051	1.01	17.30446	NA	NA	0.549032	0.0022554	56632826	99.89414	NA	NA	70.47	14822076	NA	NA	NA	NA	NA	NA
desantis	ctrl_3	39635903	75448922	75448922	39635903	100	19795267	0.0001564	1.00	36.44447	NA	NA	0.265744	0.0021035	35813019	99.88554	NA	NA	81.60	16465064	NA	NA	NA	NA	NA	NA
desantis	fus_1	35612797	66471955	66471955	35612797	100	17785490	0.0000883	0.99	35.21769	NA	NA	0.300553	0.0021299	30859158	99.88258	NA	NA	79.99	14476588	NA	NA	NA	NA	NA	NA
desantis	fus_2	47294523	107673051	107673051	47294523	100	23619629	0.0000349	1.02	14.42152	NA	NA	0.640610	0.0022572	60378528	99.88315	NA	NA	72.36	17684239	NA	NA	NA	NA	NA	NA
desantis	fus_3	37794691	71049470	71049470	37794691	100	18874586	0.0000409	1.03	35.62457	NA	NA	0.289365	0.0021430	33254779	99.87956	NA	NA	81.44	15659611	NA	NA	NA	NA	NA	NA
smith	ctrl_1	56523441	63212608	63212608	56523441	100	28252066	0.0000000	1.14	76.33318	NA	NA	0.101840	0.0020922	6689167	99.96584	NA	NA	92.92	26581477	NA	NA	NA	NA	NA	NA
smith	ctrl_2	72973159	81543822	81543822	72973159	100	36477011	0.0000033	1.12	75.04343	NA	NA	0.119042	0.0019577	8570663	99.97378	NA	NA	93.03	34320173	NA	NA	NA	NA	NA	NA
smith	tardbp_1	81164834	89990577	89990577	81164834	100	40567587	0.0000155	1.11	78.09236	NA	NA	0.091812	0.0021474	8825743	99.96346	NA	NA	93.09	38444351	NA	NA	NA	NA	NA	NA
smith	tardbp_2	81670004	90694956	90694956	81670004	100	40820246	0.0000123	1.12	77.78844	NA	NA	0.094052	0.0022170	9024952	99.96386	NA	NA	93.10	38679666	NA	NA	NA	NA	NA	NA
smith	tardbp_3	68577024	76199035	76199035	68577024	100	34276814	0.0000219	1.11	78.46129	NA	NA	0.085099	0.0020722	7622011	99.96588	NA	NA	93.10	32467252	NA	NA	NA	NA	NA	NA
bhinge	iso_1	49358770	62447827	62447827	49358770	100	49358770	0.0000268	1.06	NA	NA	NA	0.455262	0.0016714	13089057	0.00000	NA	NA	89.15	44074145	0.9649444	NA	49	100.00000	15.58140	49
bhinge	iso_2	57907498	75011913	75011913	57907498	100	57907498	0.0000169	1.07	NA	NA	NA	0.493924	0.0016511	17104415	0.00000	NA	NA	87.86	50957825	1.0323901	NA	50	100.00000	18.07492	50
bhinge	sod1_1	57424532	74874820	74874820	57424532	100	57424532	0.0000593	1.08	NA	NA	NA	0.467025	0.0016817	17450288	0.00000	NA	NA	88.12	50682994	0.9878292	NA	50	100.00000	17.54508	50
bhinge	sod1_2	46422296	59960152	59960152	46422296	100	46422296	0.0000103	1.04	NA	NA	NA	0.472328	0.0016610	13537856	0.00000	NA	NA	88.05	40936487	1.0394206	NA	50	100.00000	16.16385	50
hawkins	ctrl_1	55732128	82244817	82244817	55732128	100	55732128	0.0001172	1.04	NA	NA	NA	0.402003	0.0022973	26512689	0.00000	NA	NA	86.11	48794129	2.8396430	NA	49	100.00000	36.13990	49
hawkins	ctrl_2	56249612	87079998	87079998	56249612	100	56249612	0.0001425	1.05	NA	NA	NA	0.446901	0.0022671	30830386	0.00000	NA	NA	84.24	48318433	3.0143122	NA	50	100.00000	40.06617	50
hawkins	fus_1	56937877	91180287	91180287	56937877	100	56937877	0.0000613	1.05	NA	NA	NA	0.434754	0.0023454	34242410	0.00000	NA	NA	83.85	48671327	3.3447031	NA	50	100.00000	39.16021	50
hawkins	fus_2	55697111	91222990	91222990	55697111	100	55697111	0.0000492	1.06	NA	NA	NA	0.473655	0.0023033	35525879	0.00000	NA	NA	82.82	46919285	3.2152090	NA	51	100.00000	42.74376	50
lee.ALS	spinal_c9orf72_1	176059847	295475531	295475531	176059847	100	176059847	0.0000603	1.04	0.00000	NA	NA	0.583518	0.0028718	119415684	0.00000	NA	NA	80.38	144676081	1.3170423	NA	48	75.49589	49.68399	48
lee.ALS	spinal_c9orf72_2	158118940	248292842	248292842	158118940	100	158118940	0.0000524	1.05	0.00000	NA	NA	0.625328	0.0026696	90173902	0.00000	NA	NA	81.79	132037661	1.5092816	NA	48	75.49558	53.24453	48
lee.ALS	spinal_c9orf72_3	165519831	397216894	397216894	165519831	100	165519831	0.0000592	1.06	0.00000	NA	NA	0.682174	0.0029370	231697063	0.00000	NA	NA	61.79	119197894	1.3272903	NA	51	75.49916	60.90015	51
lee.ALS	spinal_ctrl_1	56334539	91703261	91703261	56334539	100	28153597	0.0000924	1.04	18.87285	NA	NA	0.663619	0.0039929	35368722	99.95146	NA	NA	79.50	23895796	NA	NA	NA	NA	NA	NA
lee.ALS	spinal_ctrl_2	67107456	106347097	106347097	67107456	100	33535748	0.0000420	1.04	17.48065	NA	NA	0.696667	0.0041699	39239641	99.94641	NA	NA	80.24	28822340	NA	NA	NA	NA	NA	NA
lee.ALS	spinal_ctrl_3	57737133	107257696	107257696	57737133	100	28847016	0.0004675	1.18	12.25616	NA	NA	0.746278	0.0043442	49520563	99.92535	NA	NA	74.28	23174968	NA	NA	NA	NA	NA	NA
lee.ALS	spinal_sod1_1	130130020	224968136	224968136	130130020	100	130130020	0.0000244	1.07	0.00000	NA	NA	0.590068	0.0027903	94838116	0.00000	NA	NA	80.01	106453731	0.6998293	NA	48	75.51113	50.05608	48
lee.ALS	spinal_sod1_2	177533609	254297645	254297645	177533609	100	177533609	0.0000394	1.06	0.00000	NA	NA	0.624196	0.0026957	76764036	0.00000	NA	NA	84.00	151337173	1.5103653	NA	48	75.46761	53.56905	48
lee.ALS	spinal_sod1_3	152556502	215300982	215300982	152556502	100	152556502	0.0000365	1.09	0.00000	NA	NA	0.634475	0.0026854	62744480	0.00000	NA	NA	83.98	130245147	1.7993886	NA	48	75.49433	54.11551	48

Fig 1 Pipeline schematic

PCA

ipsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
  mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS",  dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~  dataset), library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero"), #dataset = gsub("\\."," ",dataset), #dataset = str_to_title(dataset),
         DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~  DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
         ) %>%
  left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))

# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, shape = library_type)) + geom_point(aes(color=dataset), size=1) +
  scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
  theme_oz() + theme(legend.text=element_text(size=8), legend.title=element_text(size=7), legend.position = "right", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
  ggforce::geom_mark_ellipse(aes(label = library_type), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE) + guides(color=guide_legend(title="Dataset", keywidth=0.1, keyheight=0.15, default.unit="inch"))
ipsc_mn_als_datasets_with_lee.pca_dataset

Cell type marker heatmap

astrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB",  "FGFR3",  "SLC4A4", "DIO2")
endo.markers = c("CLDN5",  "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG",  "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")

undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")

nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")    
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#"NEFH",
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3") 
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>% 
  mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers", 
                           gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers", 
                           gene_name %in% mn.markers ~ "mn.markers"), 
         group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))

### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered

celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = celltype.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = celltype.markers.df.filt$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL, 
          show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6), 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),  labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmap

Fig S2-3 PCA

Fig S1 is the PRISMA flow diagram

PC1 & PC2 gene loadings

ipsc_mn_als_datasets_with_lee.vsd.rv <- rowVars(assay(ipsc_mn_als_datasets_with_lee.vsd)) # calculate the variance for each gene
ipsc_mn_als_datasets_with_lee.vsd.ntop_genes <- order(ipsc_mn_als_datasets_with_lee.vsd.rv, decreasing=TRUE)[seq_len(min(500, length(ipsc_mn_als_datasets_with_lee.vsd.rv)))] # select the ntop genes by variance
ipsc_mn_als_datasets_with_lee.vsd.pca <- prcomp(t(assay(ipsc_mn_als_datasets_with_lee.vsd)[ipsc_mn_als_datasets_with_lee.vsd.ntop_genes,])) # perform a PCA on the data in assay(x) for the selected genes
ipsc_mn_als_datasets_with_lee.vsd.loadings <- as_tibble(ipsc_mn_als_datasets_with_lee.vsd.pca$rotation, rownames = "gene_id") %>% left_join(gene2ens) %>% arrange(PC1) %>% select(gene_name, gene_id, everything())

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2")#,"ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
neuronal.markers = c(nonspecific.neuronal, dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain)

# scatter all PC1 vs PC2
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatter = ggplot(ipsc_mn_als_datasets_with_lee.vsd.loadings, aes(x = PC1, y = PC2 )) + 
    labs(x = "PC1 gene loading", y = "PC2 gene loading") +
    geom_hline(yintercept = 0, linetype = 3) + geom_vline(xintercept = 0, linetype = 3) +
    geom_point(size = 1, alpha = 0.1) +
    scale_fill_continuous(type = "viridis") +
    guides(fill = FALSE) +
    theme_oz() +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^H[1-9]",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^SNOR|RN7SK|RMRP|RPPH1",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings,  gene_name %in% c(neuronal.markers, HOX.markers)), aes(x = PC1, y = PC2, label = gene_name), colour = "black", size = 2.3) +
  annotate("text", x = 0.04, y = 0.05, label = "PC1+ PC2+",size = 3, color = "black") + annotate("text", x = -0.07, y = -0.12, label = "PC1- PC2-", size = 3, color = "firebrick2") + 
  annotate("text", x = 0.04, y = -0.12, label = "PC1+ PC2-", size = 3, color = "black") + annotate("text", x = -0.07, y = 0.05, label = "PC1- PC2+", size = 3, color = "black")
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatter

Sample characteristics

ipsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
  mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS",  dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~  dataset), 
         DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~  DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
         library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","mitchell","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero")) %>%
  left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))

# multiqc stats
multiqc_general_stats_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_general_stats_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), 
     # multiqc_general_stats_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_general_stats_stat_paths)
     ) %>% pull(multiqc_general_stats_stat_paths)
multiqc_general_stats.tsv = multiqc_general_stats_stat_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_general_stats.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_general_stats <- map_dfr(multiqc_general_stats.tsv, bind_rows, .id = "database_dir") %>% clean_names()
multiqc_rseqc_read_distribution_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_rseqc_read_distribution_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"),
     # multiqc_rseqc_read_distribution_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_rseqc_read_distribution_paths)
     ) %>% pull(multiqc_rseqc_read_distribution_paths)
multiqc_rseqc_read_distribution.tsv = multiqc_rseqc_read_distribution_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_rseqc_read_distribution.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_rseqc_read_distribution <- map_dfr(multiqc_rseqc_read_distribution.tsv, bind_rows, .id = "database_dir") %>% clean_names()
ipsc_mn_als_datasets_with_lee.pcaData = ipsc_mn_als_datasets_with_lee.pcaData %>% left_join(multiqc_general_stats) %>% left_join(multiqc_rseqc_read_distribution) # need unique sample names - If multiple dataset names within a single multiqc_general_stats.txt then will only join the first dataset name

# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=dataset)) + geom_point(size=1) +
  scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
  theme_oz() + theme(legend.position = "none") + guides(color=guide_legend(keywidth=0.5, keyheight=0.5, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
  ggforce::geom_mark_ellipse(aes(label = dataset), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE)
ipsc_mn_als_datasets_with_lee.pca_dataset

# Colour by library_type
ipsc_mn_als_datasets_with_lee.pca_library_type <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=library_type)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))+labs(colour="Library preparation")
ipsc_mn_als_datasets_with_lee.pca_library_type

# Colour by instrument
ipsc_mn_als_datasets_with_lee.pca_instrument <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=instrument)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_blank(), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_instrument

# Colour by DIV
ipsc_mn_als_datasets_with_lee.pca_DIV <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=DIV)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top"))  + labs(color="Days in vitro") + 
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_DIV

# Colour by ALS
ipsc_mn_als_datasets_with_lee.pca_als <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=condition)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_als

# Colour by mutation
ipsc_mn_als_datasets_with_lee.pca_mutation <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=mutation)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_mutation

# Colour by gender
ipsc_mn_als_datasets_with_lee.pca_gender <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=gender)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) 
ipsc_mn_als_datasets_with_lee.pca_gender

RNAseq QC metrics

Fig S3

# Colour by strandedness
ipsc_mn_als_datasets_with_lee.pca_strandedness <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=strandedness)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.2, keyheight=0.2, default.unit="inch")) + 
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_strandedness

# Colour by read depth
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_raw_total_sequences)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6, angle = 0), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(1, 'cm'))  + 
  guides(color = guide_colourbar(title = "read depth", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_raw_total_sequences,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences

# Color by intronic read % intron_read_pct
ipsc_mn_als_datasets_with_lee.pca_read_distribution <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=introns_tag_pct)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "intronic reads %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$introns_tag_pct,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) 
ipsc_mn_als_datasets_with_lee.pca_read_distribution

# Colour by biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "ribosomal rna %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna

# Colour by quali_map_mqc_generalstats_qualimap_5_3_bias
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_5_3_bias)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "5' 3' bias", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=1, low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias

# Colour by quali_map_mqc_generalstats_qualimap_reads_aligned
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_reads_aligned)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Reads aligned", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$quali_map_mqc_generalstats_qualimap_reads_aligned,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned

# Colour by picard_mqc_generalstats_picard_percent_duplication
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=picard_mqc_generalstats_picard_percent_duplication)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Read duplication %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$picard_mqc_generalstats_picard_percent_duplication,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +  
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication

# Colour by samtools_mqc_generalstats_samtools_reads_mapped
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_reads_mapped)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
  guides(color = guide_colourbar(title = "Reads mapped", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_reads_mapped,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped

# Colour by star_mqc_generalstats_star_uniquely_mapped_percent
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percent <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=star_mqc_generalstats_star_uniquely_mapped_percent)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Reads uniquely mapped %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$star_mqc_generalstats_star_uniquely_mapped_percent,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percent

Fig S4-9 Heatmap expression

Cell type marker heatmap

astrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB",  "FGFR3",  "SLC4A4", "DIO2")
endo.markers = c("CLDN5",  "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG",  "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")

undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")

nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")    
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") 
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3") 
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>% 
  mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers", 
                           gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers", 
                           gene_name %in% mn.markers ~ "mn.markers"), 
         group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))

### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered

celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = celltype.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = celltype.markers.df.filt$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL, 
          show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6), 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),  labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmap

Neuron type markers

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#,"NEFH"
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3","ETV1", "NOS1","RUNX1","NOTCH1","ARHGAP36","SLC10A4","POU3F1","FOXP2","ISL2") #
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")#dl.domains LDB1 "LHX1","POU4F1",,"LBX1""LHX2","LHX9","DRGX","LMX1B","VSX2","EVX2","LMO4"
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

neuron.type.markers = c(motor.neuron.progenitor, postmitotic.motor.neuron, nonspecific.neuronal,interneuron.markers) 
neuron.type.markers.df = tibble("gene_name" = neuron.type.markers) %>% filter(gene_name %in% neuron.type.markers) %>% 
  mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% motor.neuron.progenitor ~ "motor.neuron.progenitor", 
                           gene_name %in% postmitotic.motor.neuron ~ "postmitotic.motor.neuron", #gene_name %in% oculomotor.markers ~ "oculomotor.markers", 
                           gene_name %in% interneuron.markers ~ "interneuron"), 
         group = factor(group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuron.type.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% neuron.type.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = neuron.type.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
neuron.type.markers.df.filt = neuron.type.markers.df %>% filter(gene_name %in% neuron.type.markers.marker$gene_name)
neuron.type.markers.marker.mat <- make_matrix(select(neuron.type.markers.marker,-gene_name), pull(neuron.type.markers.marker,gene_name))

### Cluster samples ###
neuron.type.markers.rnaseq.heatmap <- Heatmap(t(neuron.type.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = neuron.type.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = factor(neuron.type.markers.df.filt$group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron")),
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",4)), labels = c("nonspecific\nneuronal", "motor neuron\nprogenitor", "postmitotic\nmotor neuron", "interneuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          column_title = NULL, 
          show_row_names = FALSE,
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
neuron.type.markers.rnaseq.heatmap

Dorso-ventral markers

Markers are from Fig 2 in https://journals.biologists.com/dev/article/148/15/dev199711/271192/Single-cell-transcriptome-profiling-of-the-human

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

neuronal.markers = c(dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain) #nonspecific.neuronal
neuronal.markers.df = tibble("gene_name" = neuronal.markers) %>% 
  mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% dl.domains ~ "dl.domains", 
                           gene_name %in% V0.domain ~ "V0.domain", gene_name %in% V1 ~ "V1", 
                           gene_name %in% V2a.domain ~ "V2a.domain", gene_name %in% V2b.domain ~ "V2b.domain", gene_name %in% MN.domain ~ "MN.domain", gene_name %in% V3.domain ~ "V3.domain"), 
         group = factor(group, levels = c("dl.domains","V0.domain", "V1", "V2a.domain", "V2b.domain", "MN.domain", "V3.domain"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuronal.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% neuronal.markers.df$gene_name) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = neuronal.markers.df$gene_name)) %>% select(-gene_id) %>%
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% select(-contains("answerals_CASE"))
neuronal.markers.marker.mat <- make_matrix(select(neuronal.markers.marker,-gene_name), pull(neuronal.markers.marker,gene_name))

### Cluster samples ###
neuronal.markers.marker.centered_mat = t(scale(t(neuronal.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
dorsoventral.markers.heatmap <- Heatmap(t(neuronal.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
          column_order = neuronal.markers.df$gene_name,
          column_names_gp = gpar(fontsize = 7), 
          column_split = neuronal.markers.df$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",7)), labels =  c("dl\ndomains","V0\ndomain", "V1", "V2a\ndomain", "V2b\ndomain", "MN\ndomain", "V3"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          column_title = NULL, column_title_gp = gpar(fontsize = 8), 
          cluster_columns = FALSE, cluster_column_slices = FALSE, 
          cluster_rows = FALSE,
          row_title = NULL, 
          row_split = dataset.samples.df$dataset,
          show_row_names = FALSE, 
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)))
dorsoventral.markers.heatmap

Rostro-caudal markers

HOX markers

HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
HOX.markers.df <- data.frame(row.names = HOX.markers, gene_name = HOX.markers) %>% 
  mutate(group = gsub("HOX[A-D]","", gene_name), group = factor(as.numeric(gsub("-AS$","", group)))) %>% 
  arrange(group) %>% 
  mutate(level = factor(case_when(group %in% c(1,2,3) ~ "Hindbrain", group %in% c(4,5,6,7) ~ "Cervical", group %in% c(8,9) ~ "Thoracic", 
                                  group %in% c(10,11) ~ "Lumbar", TRUE ~ "Sacral"), levels = c("Hindbrain","Cervical","Thoracic","Lumbar","Sacral")))
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
HOX.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% distinct(gene_name, .keep_all = TRUE) %>% 
  filter(gene_name %in% HOX.markers.df$gene_name) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>% 
  arrange(factor(gene_name, levels = HOX.markers.df$gene_name)) %>% select(-gene_id) %>%
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
HOX.markers.marker.mat <- make_matrix(select(HOX.markers.marker,-gene_name), pull(HOX.markers.marker,gene_name))
HOX.markers.marker.centered.mat = t(scale(t(HOX.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
HOX.markers.heatmap <- Heatmap(t(HOX.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
          column_order = HOX.markers.df$gene_name,
          column_names_gp = gpar(fontsize = 7), 
          column_split = HOX.markers.df$level,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Hindbrain", "Cervical", "Thoracic","Lumbar","Sacral"), labels_gp = gpar(fontsize = 8), labels_rot = 0)),
          column_title = NULL, column_title_gp = gpar(fontsize = 8), 
          cluster_columns = FALSE, cluster_column_slices = FALSE, 
          cluster_rows = FALSE,
          row_title = NULL, 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          show_row_names = FALSE, 
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",17)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)))
HOX.markers.heatmap